MPR¶

MLModule¶

genre	`Resample`
author	`MeVis Medical Solutions AG`
package	`MeVisLab/Standard`
dll	`MLResample1`
definition	MLResample1.def
see also	`MPRPath`, `Reformat`
inherits from	`MPRLight`
keywords	`multi`, `planar`, `reformat`, `interaction`, `oblique`

Purpose¶

The module MPR calculates a multi-planar reformatted image from its input image.

The reformatting requires sampling of the input image, which can be done with different filters. The MPR is optimized (using fixpoint arithmetic) for int8 and int16 types, but has a fallback implementation for the other basic datatypes.

Depending on the Memory Access mode, it uses different strategies to access the input image.

Usage¶

The MPR outputs a reformatted slice (or a slice stack if the Size parameter is != 1) that is defined by its center world position (Translation) and a Rotation.

The edge length of the reformatted output slices is given by the Field Of View parameter (in mm), the resolution is specified by the Output Size parameter (in pixels).

Example¶

Details¶

The coordinate system of the output image is defined by coordinate vectors wx, wy and wz, denoting the direction of the image’s pixel rows and columns and the depth direction, respectively. These vectors are computed from the Rotation parameter R by

(wx, wy, wz) = R (ex, ez, -ey),

where ex, ey and ez are the unit vectors. This definition, especially the swapping of the Y and Z direction, is compatible to the conventions used for Open Inventor draggers, which define the Y-axis as the direction normal. Accordingly, the translation and rotation fields of an Inventor Dragger (e.g. SoJackDragger, SoPlaneDragger) can directly be connected to the fields of an MPR module.

In order to obtain the MPR rotation parameter for a given plane normal, compute:

rotation = SbRotation(SbVec3f(0,1,0), planeNormal);

If three points p1, p2 and p3 on a plane are given, the plane normal can be computed using the cross product:

SbVec3f dir1 = p2-p1;
SbVec3f dir2 = p3-p1;
SbVec3f planeNormal = dir1.cross(dir2);

The voxel-to-world-matrix W of the MPR’s output image is computed from the rotation R and the translation T by

W = T R M S D,

where

D describes the translation from image center to origin (-sx/2, -sy/2, 0),

S describes the voxel size, and

M rotates y to z and z to -y.

Here is the corresponding code snippet:

double voxelSize = fieldOfView / outputSize;
dir1 = rotation * vec3(1, 0, 0) * voxelSize;
dir2 = rotation * vec3(0, 0, 1) * voxelSize;
dir3 = rotation * vec3(0, -1, 0) * voxelSize;

vec3 trans = translation - outputSize/2*dir1 - outputSize/2*dir2 - 1/2*dir3;

toWorldMatrix = mat4(dir1, dir2, dir3, trans);

../../../Modules/ML/MLResample1/mhelp/Images/MPRDefinition.jpg

The above figure shows an input image box drawn in world coordinates and an MPR slice that defines an oblique slice within this box.

The center of the slice is given as the Translation parameter, the slice normal is given by the Rotation applied to the negative world Y-axis.

Windows¶

Default Panel¶

../../../Modules/ML/MLResample1/mhelp/Images/Screenshots/MPR._default.png

Input Fields¶

input0¶

name: input0, type: Image¶: Input image from which an MPR is computed.

Output Fields¶

output0¶

name: output0, type: Image¶: Provides the MPR image slice (or slice stack if Size > 1).

outputSlice¶

name: outputSlice, type: SoNode¶: An Open Inventor scene representing the MPR slice in 3D (see the Inventor parameter section for relevant options).

Parameter Fields¶

Field Index¶

`Activate clip plane`: `Bool`	`Enable`: `Bool`	`pageSizeX`: `Integer`
`Alpha`: `Float`	`Enable Current Slice`: `Bool`	`pageSizeY`: `Integer`
`Aspect Ratio`: `Double`	`Enable Plane Edit`: `Bool`	`Plane`: `Plane`
`Auto Center`: `Bool`	`Field Of View`: `Double`	`Represent Input Slice`: `Trigger`
`Axial (axial)`: `Trigger`	`Field Of View X`: `Double`	`Rotation`: `Rotation`
`Axial (axialOnInput)`: `Trigger`	`Field Of View Y`: `Double`	`Sagittal (sagittal)`: `Trigger`
`Blend Mode`: `Enum`	`Fill Value`: `Double`	`Sagittal (sagittalOnInput)`: `Trigger`
`Border Color`: `Color`	`Flip Clip Plane`: `Bool`	`Size`: `Double`
`Border Handling`: `Enum`	`Image Color`: `Color`	`Size In Slices`: `Integer`
`centeredTranslation`: `Vector3`	`Interactive manipulator`: `Bool`	`Slice No.`: `Integer`
`Clip Plane Offset`: `Float`	`Interpolation`: `Enum`	`Snap Current Slice To Integer If Orthogonal`: `Bool`
`Coronal (coronal)`: `Trigger`	`Memory Access`: `Enum`	`Time Projection`: `Enum`
`Coronal (coronalOnInput)`: `Trigger`	`Mode`: `Enum`	`Time Span`: `Integer`
`Current Slice`: `Double`	`Number Of Slices`: `Integer`	`Time Start`: `Integer`
`currentSliceMax`: `Integer`	`On (borderOn)`: `Bool`	`Translation`: `Vector3`
`currentSliceMin`: `Integer`	`On (drawImageOn)`: `Bool`	`Up Vector`: `Vector3`
`currentSliceRounded`: `Integer`	`Output Size`: `Integer`	`Use Up Vector`: `Bool`
`Depth Projection`: `Enum`	`Output Size Mode`: `Enum`	`Use Z buffer`: `Bool`
`disableDirectVoxelCopy`: `Bool`	`Output Size X`: `Integer`
`Draw axes`: `Bool`	`Output Size Y`: `Integer`

Visible Fields¶

Rotation¶

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

Sets the rotation of the MPR slice, mapping the world X-, Y-, and Z-axes to the MPR image’s X-, negative Z-, and Y-axes, respectively.

The easiest way to edit the rotation is to use an Open Inventor dragger and connect its rotation field to this parameter.

Translation¶

name: translation, type: Vector3, default: 0 0 0¶: Sets the translation vector to the center of the (first) MPR slice (in world coordinates).

Plane¶

name: plane, type: Plane, default: 0 0 1 0¶: Sets the plane containing the first slice of the MPR output image.

Enable Plane Edit¶

name: enablePlaneEdit, type: Bool, default: FALSE¶

If checked, the Plane field can be used as an input field.

Incremental modifications of the Plane field are transformed to modifications of the Rotation and Translation parameters.

Auto Center¶

name: autoCenter, type: Bool, default: FALSE¶: If enabled, the Translation is internally moved so that the MPR is centered on the input image box. This is especially useful in combination with Output Size Mode == ‘Automatic’ and the “Slicing” tab.

Fill Value¶

name: fillValue, type: Double, default: 0, deprecated name: fillvalue¶: Sets the value used for regions outside of the input image.

Output Size Mode¶

name: outputSizeMode, type: Enum, default: AspectRatio¶: Defines how the output size is defined.

Values:

Title	Name	Description
Aspect Ratio	AspectRatio	Uses a single size and an aspect ratio to define the output size. Only equal voxel sizes in x/y are possible.
Independent	Independent	Allows to specify output size and field-of-view in X/Y separately.
Automatic	Automatic	Determines the output size automatically to match the input image size, taking the `Rotation` to account, so that orthogonal views along the input image have the same output size as a OrthoSwapFlip/Subimage combination would have. This mode should be used when using the “Slicing” Tab. It is typically useful to also enable `Auto Center`.

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 resolution of the output slice (X,Y) in pixels.

Aspect Ratio¶

name: aspectRatio, type: Double, default: 1¶

Sets the aspect ratio of the MPR.

Values larger than 1.0 produce portrait, smaller than 1.0 landscape output.

Field Of View X¶

name: fieldOfViewX, type: Double, default: 100¶: Sets the X extent of the MPR slice in the world coordinate system (in mm).

Field Of View Y¶

name: fieldOfViewY, type: Double, default: 100¶: Sets the Y extent of the MPR slice in the world coordinate system (in mm).

Output Size X¶

name: outputSizeX, type: Integer, default: 256¶: Sets the X resolution of the output slice in pixels.

Output Size Y¶

name: outputSizeY, type: Integer, default: 256¶: Sets the Y resolution of the output slice in pixels.

Mode¶

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¶

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

Sets the slab size (depth/Z size) of the output image.

Depending on the Mode, the slab size is given in MM or in slices. At least one slice is rendered, regardless how small the slab size is set.

Size In Slices¶

name: currentSlabSizeInSlices, type: Integer, persistent: no¶: Outputs the current slab size in slices. This may change its value while rotating when a MM based Mode is used.

Use Up Vector¶

name: useUpVector, type: Bool, default: FALSE, deprecated name: forceUpright¶: If checked, the MPR is rotated such that its Y-axis becomes as close as possible to the Up Vector. (If the Up Vector is orthogonal to the MPR, no rotation will be performed.)

Up Vector¶

name: upVector, type: Vector3, default: 0 1 0¶: The up vector can be used to determine the orientation of the MPR axes within the plane. If Use Up Vector is set, the MPR will be rotated around the center (Translation) in order to align the Y-axis with the up vector.

Slice No.¶

name: inputSliceNo, type: Integer, default: 0¶: Sets the slice number to be reproduced by the Represent Input Slice trigger.

Represent Input Slice¶

name: representInputSlice, type: Trigger¶: If pressed, Field Of View, Output Size, Aspect Ratio, Translation, and Rotation are being adjusted such that the output exactly matches the input slice number Slice No..

Axial (axial)¶

name: axial, type: Trigger¶: If pressed, the MPR is set to axial (transversal) orientation in world coordinates.

Sagittal (sagittal)¶

name: sagittal, type: Trigger¶: If pressed, the MPR is set to sagittal orientation in world coordinates.

Coronal (coronal)¶

name: coronal, type: Trigger¶: If pressed, the MPR is set to coronal orientation in world coordinates.

Axial (axialOnInput)¶

name: axialOnInput, type: Trigger¶: If pressed, the MPR is set to axial (transversal) orientation on the input image. It selects an orientation of the input image that is closest to the world axial orientation. The output of the MPR will be identical to that of an OrthoSwapFlip with axial settings.

Sagittal (sagittalOnInput)¶

name: sagittalOnInput, type: Trigger¶: If pressed, the MPR is set to sagittal orientation on the input image. It selects an orientation of the input image that is closest to the world sagittal orientation. The output of the MPR will be identical to that of an OrthoSwapFlip with sagittal settings.

Coronal (coronalOnInput)¶

name: coronalOnInput, type: Trigger¶: If pressed, the MPR is set to coronal orientation on the input image. It selects an orientation of the input image that is closest to the world coronal orientation. The output of the MPR will be identical to that of an OrthoSwapFlip with coronal settings.

Interpolation¶

name: interpolation, type: Enum, default: Trilinear, deprecated name: Mode¶: Defines the interpolation used for resampling.

Values:

Title

Name

Deprecated Name

Description

Nearest Neighbor

NearestNeighbor

Nearest Neigbour

No interpolation, picks the nearest input image voxel.

Fastest mode.

Trilinear

Trilinear(skip border),TrilinearSkipBorder

Trilinear filtering. The 8-voxel-neighborhood is used for linear interpolation.

Slowest mode.

Border Handling¶

name: borderHandling, type: Enum, default: UseFillValue¶: Selects how borders are handled in trilinear filtering.

Values:

Title	Name	Description
Clamp To Edge	ClampToEdge	Clamps the interpolation to the edge of the input volume and uses the fill value only for values beyond the edge.
Use Fill Value	UseFillValue	Uses the fill value for values on the border and outside of the volume.

Memory Access¶

name: memoryAccess, type: Enum, default: Global, deprecated name: pagedInputImage¶: Defines how the module accesses the input image.

Values:

Title

Name

Deprecated Name

Description

Global

FALSE,Paged,TRUE

Fastest, but highest memory consumption and initialization time. The input image is accessed as a global image (via the ML memory image). This consumes a lot of memory for large datasets.

If not enough memory is available, the module falls back to the Virtual Volume memory 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¶: Enables the projection of the slab to a single slice. The Depth Projection and Time Projection are used to define which projection method is used.

Depth Projection¶

name: depthSlabRenderMode, type: Enum, default: Maximum¶: Selects the render mode for depth projection.

Values:

Title	Name	Description
Minimum	Minimum	Minimum value is computed.
Maximum	Maximum	Maximum value is computed.
Average	Average	Average is computed.
Keep Dimension	KeepDimension	The depth dimension is not projected, the output image will have the same number of slices as the input image.

Time Projection¶

name: timeSlabRenderMode, type: Enum, default: Maximum¶: Selects the render mode for temporal projection.

Values:

Title	Name	Description
Minimum	Minimum	Minimum value is computed.
Maximum	Maximum	Maximum value is computed.
Average	Average	Average is computed.
Keep Dimension	KeepDimension	The time dimension is not projected, the output image will have the same number of time points as the input image.

Time Start¶

name: timeSlabStart, type: Integer, default: 0¶: Selects the start time point for temporal projection.

Time Span¶

name: timeSlabSize, type: Integer, default: 1¶: Selects the number of timepoints that are projected.

Enable Current Slice¶

name: enableCurrentSlice, type: Bool, default: FALSE¶: Enables the Current Slice field and its synchronization.

Current Slice¶

name: currentSlice, type: Double, default: 0, minimum: :field:`currentSliceMin`, maximum: :field:`currentSliceMax`¶: Allows to select the current slice along the axis given by the rotation. The current slice is automatically adjusted when the Rotation of the MPR changes to cover the whole rotated input volume.

Number Of Slices¶

name: numberOfSlices, type: Integer, default: 0¶: The number of slices available under the current Rotation.

Snap Current Slice To Integer If Orthogonal¶

name: snapCurrentSliceToIntegerIfOrthogonal, type: Bool, default: TRUE¶: If enabled, the current slice is snapped to an integer when the rotation is orthogonal on the input image. This allows the MPR to directly copy input voxels instead of using interpolation in orthogonal cases.

Image Color¶

name: imageColor, type: Color, default: 1 1 1, deprecated name: baseColor¶: Sets the color used to display the image data.

Border Color¶

name: borderColor, type: Color, default: 1 1 1¶: Sets the color used to draw the slice border.

On (borderOn)¶

name: borderOn, type: Bool, default: TRUE¶: Enables/disables the drawing of the slice border.

On (drawImageOn)¶

name: drawImageOn, type: Bool, default: TRUE¶: Enables/disables the drawing of the image data.

Interactive manipulator¶

name: manipulatorOn, type: Bool, default: TRUE¶: Enables/disablse a 3D manipulator that can be used to translate, rotate and scale the MPR slice in the Inventor scene.

Activate clip plane¶

name: clipPlaneOn, type: Bool, default: FALSE¶: Enables/disables a clip plane applied to the Open Inventor scene on one side of the MPR plane.

Flip Clip Plane¶

name: flipClipPlane, type: Bool, default: FALSE¶: If checked, the halfspace that is clipped by the clip plane is flipped.

Clip Plane Offset¶

name: clipPlaneOffset, type: Float, default: 0¶: Sets an offset to the clip plane in the direction of the MPR slice normal.

Draw axes¶

name: axesOn, type: Bool, default: FALSE, deprecated name: drawVectors¶: Enables/disables drawing of the MPR output image coordinate axes.

Alpha¶

name: alphaFactor, type: Float, default: 1, minimum: 0, maximum: 1¶: Sets an alpha value used to draw the image data.

Use Z buffer¶

name: zBuffer, type: Bool, default: TRUE¶: If disabled, the z buffer is ignored when rendering the slice.

Blend Mode¶

name: blendMode, type: Enum, default: BLEND_REPLACE¶: Defines how the slice texture is drawn.

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¶

centeredTranslation¶

name: centeredTranslation, type: Vector3, persistent: no¶

pageSizeX¶

name: pageSizeX, type: Integer, default: 128¶

pageSizeY¶

name: pageSizeY, type: Integer, default: 128¶

disableDirectVoxelCopy¶

name: disableDirectVoxelCopy, type: Bool, default: FALSE¶

currentSliceRounded¶

name: currentSliceRounded, type: Integer, default: 0¶

currentSliceMin¶

name: currentSliceMin, type: Integer, default: 0¶

currentSliceMax¶

name: currentSliceMax, type: Integer, default: 0¶

MPR¶

Purpose¶

Usage¶

Example¶

Details¶

Windows¶

Default Panel¶

Input Fields¶

input0¶

Output Fields¶

output0¶

outputSlice¶

Parameter Fields¶

Field Index¶

Visible Fields¶

Rotation¶

Translation¶

Plane¶

Enable Plane Edit¶

Auto Center¶

Fill Value¶

Output Size Mode¶

Field Of View¶

Output Size¶

Aspect Ratio¶

Field Of View X¶

Field Of View Y¶

Output Size X¶

Output Size Y¶

Mode¶

Size¶

Size In Slices¶

Use Up Vector¶

Up Vector¶

Slice No.¶

Represent Input Slice¶

Axial (axial)¶

Sagittal (sagittal)¶

Coronal (coronal)¶

Axial (axialOnInput)¶

Sagittal (sagittalOnInput)¶

Coronal (coronalOnInput)¶

Interpolation¶

Border Handling¶

Memory Access¶

Enable¶

Depth Projection¶

Time Projection¶

Time Start¶

Time Span¶

Enable Current Slice¶

Current Slice¶

Number Of Slices¶

Snap Current Slice To Integer If Orthogonal¶

Image Color¶

Border Color¶

On (borderOn)¶

On (drawImageOn)¶

Interactive manipulator¶

Activate clip plane¶

Flip Clip Plane¶

Clip Plane Offset¶

Draw axes¶

Alpha¶

Use Z buffer¶

Blend Mode¶

Hidden Fields¶

centeredTranslation¶

pageSizeX¶

pageSizeY¶

disableDirectVoxelCopy¶

currentSliceRounded¶

currentSliceMin¶

currentSliceMax¶

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