Transformation

This category contains 9 operator(s).

class BinaryClose

Binary Close

Perform morphological closing on segmented objects with a given label by a spherically symmetric structuring element of a given radius.

transform(self, dataset, structuring_element_id=0, radius=1, object_label=1, background_label=0)
Parameters

  • structuring_element_id (enumeration)

    • default: 0

    • options:

      • 0 - Box

      • 1 - Ball

      • 2 - Cross

  • radius (int)

    • default: 1

    • minimum: 1

  • object_label (int)

    • default: 1

  • background_label (int)

    • default: 0

Implementation

  • Python script: BinaryClose.py

  • JSON descriptor: BinaryClose.json

class BinaryDilate

Binary Dilate

Dilate segmented objects with a given label by a spherically symmetric structuring element of a given radius.

transform(self, dataset, structuring_element_id=0, radius=1, object_label=1, background_label=0)
Parameters

  • structuring_element_id (enumeration)

    • default: 0

    • options:

      • 0 - Box

      • 1 - Ball

      • 2 - Cross

  • radius (int)

    • default: 1

    • minimum: 1

  • object_label (int)

    • default: 1

  • background_label (int)

    • default: 0

Implementation

  • Python script: BinaryDilate.py

  • JSON descriptor: BinaryDilate.json

class BinaryErode

Binary Erode

Erode segmented objects with a given label by a spherically symmetric structuring element of a given radius.

transform(self, dataset, structuring_element_id=0, radius=1, object_label=1, background_label=0)
Parameters

  • structuring_element_id (enumeration)

    • default: 0

    • options:

      • 0 - Box

      • 1 - Ball

      • 2 - Cross

  • radius (int)

    • default: 1

    • minimum: 1

  • object_label (int)

    • default: 1

  • background_label (int)

    • default: 0

Implementation

  • Python script: BinaryErode.py

  • JSON descriptor: BinaryErode.json

class BinaryMinMaxCurvatureFlow

Binary Min Max Curvature Flow

This filter smooths a binary image by evolving a level set with a curvature-based speed function.

transform(self, dataset, stencil_radius=2, iterations=10, threshold=50.0)
Parameters

  • stencil_radius (int)

    • default: 2

    • minimum: 1

  • iterations (int)

    • default: 10

    • minimum: 1

  • threshold (double)

    • default: 50.0

    • minimum: 0.0

Implementation

  • Python script: BinaryMinMaxCurvatureFlow.py

  • JSON descriptor: BinaryMinMaxCurvatureFlow.json

class BinaryOpen

Binary Open

Perform morphological opening on segmented objects with a given label by a spherically symmetric structuring element of a given radius.

transform(self, dataset, structuring_element_id=0, radius=1, object_label=1, background_label=0)
Parameters

  • structuring_element_id (enumeration)

    • default: 0

    • options:

      • 0 - Box

      • 1 - Ball

      • 2 - Cross

  • radius (int)

    • default: 1

    • minimum: 1

  • object_label (int)

    • default: 1

  • background_label (int)

    • default: 0

Implementation

  • Python script: BinaryOpen.py

  • JSON descriptor: BinaryOpen.json

class Pad_Data

Pad Volume

Enlarge the volume by padding it with additional voxels.

transform(dataset, pad_size_before=[0, 0, 0], pad_size_after=[0, 0, 0], pad_mode_index=0)
Parameters

  • unknown (xyz_header)

  • pad_size_before (int) - Additional padding on the lower-index side of each dimension.

    • default: [0, 0, 0]

    • minimum: [0, 0, 0]

    • maximum: [999, 999, 999]

  • pad_size_after (int) - Additional padding on the higher-index side of each dimension.

    • default: [0, 0, 0]

    • minimum: [0, 0, 0]

    • maximum: [999, 999, 999]

  • pad_mode_index (enumeration) - Padding mode

    • default: 0

    • options:

      • 0 - Constant Zero

      • 1 - Edge

      • 2 - Wrap

      • 3 - Minimum

      • 4 - Median

Implementation

  • Python script: Pad_Data.py

  • JSON descriptor: Pad_Data.json

class Resample

Resample

Rescale the voxel spacing according to a resampling factor.

transform(dataset, resampling_factor=[1, 1, 1])
Parameters

  • unknown (xyz_header)

  • resampling_factor (double)

    • default: [1, 1, 1]

    • minimum: [0.01, 0.01, 0.01]

    • maximum: [100, 100, 100]

    • precision: 2 decimal places

Implementation

  • Python script: Resample.py

  • JSON descriptor: Resample.json

class Rotate3D

Rotate

Rotate dataset along a given axis.

transform(dataset, rotation_angle=90.0, rotation_axis=0)
Parameters

  • rotation_angle (double) - Rotation angle in degrees.

    • default: 90.0

    • minimum: -360.0

    • maximum: 360.0

  • rotation_axis (enumeration) - Axis of rotation.

    • default: 0

    • options:

      • 0 - X

      • 1 - Y

      • 2 - Z

Implementation

  • Python script: Rotate3D.py

  • JSON descriptor: Rotate3D.json

class SwapAxes

Swap Axes

Swap two axes in the dataset.

transform(dataset, axis1, axis2)
Parameters

  • axis1 (enumeration) - First axis

    • default: 0

    • options:

      • 0 - X

      • 1 - Y

      • 2 - Z

  • axis2 (enumeration) - Second axis

    • default: 2

    • options:

      • 0 - X

      • 1 - Y

      • 2 - Z

Implementation

  • Python script: SwapAxes.py

  • JSON descriptor: SwapAxes.json