Purpose

The module SliceDistanceTransform computes the distance from each voxel midpoint to the border of an object defined by a mask or by contours (CSOs) on slices where the object is defined.

Additionally, the module SliceDistanceTransform can optionally interpolate those distances on slices between the slices where the object is defined.

Usage

To estimate the shape of an object from sparsely spaced slices using ‘Shape Based Interpolation,’ as described in the referenced paper, select a Distance Mode based on the available input and choose Interpolate Slices.

The module SliceDistanceTransform can also be utilized to create a smooth surface from CSOs, such as contours read from an RT Struct.

Disable Interpolate Slices in this case and use Distance Mode Contours Chamfer or Contours Exact. Connect a WEMIsoSurface to output0 to create a WEM from the contours.

The WEMIsoSurface should set WEMIsoSurface.useMinValue to TRUE, and set WEMIsoSurface.useMaxValue to FALSE, and use a small negative value as WEMIsoSurface.isoMaxValue in order to generate a surface with distance close to 0 to the contours or the input mask borders:

../../../Projects/SliceDistanceTransform/Modules/mhelp/Images/Screenshots/WEMIsoSurfaceParameters.png

Details

The algorithm is based on ‘method 5’ (with linear between-slice interpolation) described in:

G. Herman et al: Shape-based Interpolation, IEEE Computer Graphics&Applications, vol. 12 no. 3 p.69-79.

The original algorithm, as described in the paper, initializes the pixels adjacent to the object border with static distance values and subsequently distributes these values to the remaining pixels of the slice using a fast two-phase chamfering algorithm. This approach is applied when using Distance Mode Input Image Mask.

If using Distance Mode Contours Chamfer, this module initializes the border pixels with the exact distance to the contours instead of using initial static integer distance values on a binary mask. This yields higher distance precision, especially near the contours. The chamfering process remains the same, except when Distance Mode Contours Exact is checked. In this case, the chamfering process is skipped, and the exact distance to the contours is calculated for all pixels of slices where the contours are defined. However, this process takes significantly longer.

Distances are calculated in world space, in contrast to the algorithm presented in the referenced paper.

The computed distances are signed, with distances outside the contours being positive and distances inside the contours being negative.

For the Distance Mode Contours Chamfer, the given contours are internally voxelized on the slices where they are defined, equivalent to using CSOVoxelizeContours in XOR mode, with BorderHandling set to Midpoint. For both Distance Mode Contours Chamfer and Contours Exact, there is no need to voxelize the contours into the input image beforehand, as the content of the input image is ignored in these modes.

Time points are not handled by SliceDistanceTransform. Please use a combination of SubImage and CSOFilter to manage the time points correctly. The module SliceDistanceTransform outputs an image with only one time point and treats the CSOs of all given time points as if they had the same time point.

Windows

Default Panel

../../../Projects/SliceDistanceTransform/Modules/mhelp/Images/Screenshots/SliceDistanceTransform._default.png

Input Fields

input0

name: input0, type: Image

The input image is used solely as a binary mask or as a reference grid, respectively.

For Distance Mode Input Image Mask, the image is interpreted as a binary mask, where voxels with a value of 0 are considered background, and all other values are regarded as foreground.

For both Contours Chamfer and Contours Exact, only the image’s extent, voxel size, and world-to-voxel matrix are utilized; the actual voxel values are not used.

inCSOList

name: inCSOList, type: CSOList(MLBase)

The input CSOList; this input is not used in Distance Mode Input Image Mask.

The CSOs must lie in the axial voxel plane of the input image and must be closed.

CSOs above and below the input image in the z-direction (in voxel space) are not considered. CSOs beside the input image (in the x/y direction in voxel space) are only considered in Distance Mode Contours Exact.

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

Output Fields

output0

name: output0, type: Image

Distance image, where the voxel values represent the distances to the given contours or the mask border on a slice. Voxels inside the contours have a negative sign, voxels outside the contours have a positive sign.

Parameter Fields

Field Index

Clear: Trigger
Distance Mode: Enum
Interpolate Slices: Bool
Update: Trigger
Update Mode: Enum
Value for non-interpolated slices: Float

Visible Fields

Update Mode

name: updateMode, type: Enum, default: Clear

Defines the update behavior of the module, reacting to changes of any input or parameter field (except Update Mode itself).

Values:

Title Name Description
Off Off The module does not change its output.
Clear Clear The module clears its output.
Update Update The module computes anew.

Interpolate Slices

name: interpolateSlices, type: Bool, default: FALSE

If checked, the module interpolates the distances on the slices between those where contours are defined.

Otherwise, only the distances on the slices where contours or masks are defined are computed.

Value for non-interpolated slices

name: valueForNonInterpolatedSlices, type: Float, default: 0

Sets a distance value that is written into voxels on slices that are not interpolated.

These slices are those between the slices where contours are defined if the option Interpolate Slices is off; in any case, all slices above the first and below the last slices where contours are defined.

Distance Mode

name: distanceMode, type: Enum, default: InputImageMask

Defines the algorithm used for distance calculation.

Values:

Title Name Description
Input Image Mask InputImageMask

Calculates distances to the border between background (voxel value equals 0) and foreground voxels (voxel value not equal to 0) in the input mask image on slices where the mask is defined, using a fast two-phase chamfering algorithm.

If this mode is used, the input contours are not considered at all.
Contours Chamfer ContoursChamfer

Calculates exact distances to the input contours for voxels ‘touching’ the contours and distributes these distances on slices where the contours are defined, using a fast two-phase chamfering algorithm.

If this mode is used, the content of the input image mask is not considered at all.
Contours Exact ContoursExact

Calculates exact distances to the input contours for all voxels on slices where the contours are defined.

If this mode is used, the content of the input image mask is not considered at all.

Update

name: update, type: Trigger

When pressed, the module computes anew.

Clear

name: clear, type: Trigger

When pressed, the module clears and invalidates its output image.