Operations List

List of all classes implementing the Operation interface. More...

Collaboration diagram for Operations List:

Detailed Description

List of all classes implementing the Operation interface.

Classes
class	InverseOperation
	Operation that inverts a specific operation by using the InversionComponent. More...
class	AddCenterBoxOperation
	Add Centerbox in a second channel. More...
class	AddPixelwisePredictionChannelOperation
	Run an existing pixelwise model and add result to the input image as additional channels. More...
class	AddPositionChannelOperation
	Add Position Channel. More...
class	AddRandomNoiseOperation
	Apply a pixelwise random noise to the image pixels type (string): Distribution of the noise ('uniform', 'gaussian', 'gamma') random_range (double): The generated noise level: For 'uniform': noise is drawn in [-intensity, intensity] For 'gaussian': noise is drawn from a Gaussian with zero mean and standard deviation equal to intensity For 'gamma': noise is drawn from a Gamma distribution with k = theta = intensity (note that this noise has a mean of 1.0 so it is biased) For 'shot': noise is drawn from a Gaussian with zero mean and standard deviation equal to intensity * sqrt(pixelValue) probability (double): Value in [0.0; 1.0] indicating the probability of this operation to be performed. More...
class	AdjustShiftScaleOperation
	Apply a shift and scale to the input image intensities: Output = (Input + shift) / scale. More...
class	ApplyTopDownFlagOperation
	Flip the image, if the image is not top-down. More...
class	ApproximateToHigherResolutionOperation
	Replicate the input from the original reference image. More...
class	ArgMaxOperation
	Create a label map with the indices corresponding of the input channel with the highest value. More...
class	AxisFlipOperation
	Flip image content along specified set of axes. More...
class	AxisRotationOperation
	Rotate around image axis with axis-specific rotation angles that are signed multiples of 90 degrees. More...
class	BakeDeformationOperation
	Deform an image with its attached Deformation and store the result into the returned output image. More...
class	BakePhotometricInterpretationOperation
	The PhotometricInterpretation is a DICOM flag that encodes the relation between intensity values and their display value If the PhotometricInterpretation is set to Monochrome1, we invert the values over the range of values (min becomes max, max becomes min). More...
class	BakeTransformationOperation
	Apply the rotation contained in the matrix of the input volume. More...
class	BlobsFromKeypointsOperation
	Transforms keypoints into an actual image (blob map with the same size of the image). More...
class	CheckDataOperation
	Runs some tests on the input data and then forwards it as is. More...
class	ClipOperation
	Clip values in a range. More...
class	ConvertSlicesToVolumeOperation
	Creates a volume out of a set of slices with the same size. More...
class	ConvertToGrayOperation
	Convert input image to grayscale by averaging the color channels. More...
class	ConvertVolumeToSlicesOperation
	Extract slices from a volume TODO: for now this works only if input SIS contains a single 3D image, see issue ML-577. More...
class	ConvolutionalCRFOperation
	Adapt segmentation map or raw output of model to image content. More...
class	CopyOperation
	Copy a set of fields of a DataItem source (List[str]): list of the elements to be copied target (List[str]): list of the names of the new elements (must match the size of source) More...
class	CropAroundLabelMapOperation
	Selects the given label from a multi-label, and crops the image and labels around it. More...
class	AddDegradedLabelAsChannelOperation
	Operation to add a channel with blobs whose sign depends on the label. More...
class	CropOperation
	Crop input images and label maps with a given size and offset crop_size (vec3i): List of integers representing the target dimensions of the image to be cropped. More...
class	CutOutOperation
	Cut out regions in input images and label maps with a given size, offset and fill value size (vector<vec3>): List of 3-dim vectors representing the extent of the cut out fill_value (vector<float>): List of intensity values for filling out cutout region size_units (ParamUnit): Units of cut out size parameter. More...
class	DeformationOperation
	Apply a deformation to the image using a specified control point grid and specified displacements nSubdivisions (vec3i): list specifying the number of subdivisions for each dimension (the number of control points is subdivisions+1). More...
class	EnsureExplicitMaskOperation
	Converts the existing mask of all input images into explicit masks. More...
class	EnsureOneToOneMatrixMappingOperation
	Ensures that it is possible to get/set the matrix of each frame of the input image set independently. More...
class	ExtractRandomSubsetOperation
	Extracts a random subset from a SharedImageSet. More...
class	ExtractSubsetOperation
	Extracts a subset from a SharedImageSet. More...
class	GammaCorrectionOperation
	Apply a gamma correction which changes the overall contrast (see https://en.wikipedia.org/wiki/Gamma_correction) gamma (double): Power applied to the normalized intensities. More...
class	GenerateRandomKeypointsOperation
	Generate uniformly distributed random keypoints in the image. More...
class	HighPassOperation
	Smooth input image with a Gaussian kernel with halfKernelSize Then subtract the smoothed image from the input, resulting in a reduction of low-frequency components (like large gradients) More...
class	ImageMattingOperation
	Reshape label map based on intensities of input image. More...
class	InvertOperation
	Invert the intensities of the image. More...
class	KeypointsFromBlobsOperation
	Extracts keypoints from a blob image Requires an image called label keypoints_field_name (str): Field name of the output keypoints keypoint_extraction_mode (int): Extraction mode: 0: Max, 1: Mean, 2: Local Max. More...
class	KeepLargestComponentOperation
	Create a label map with the largest components above the specified threshold. More...
class	ForegroundGuidedLabelUpsamplingOperation
	Operation that generates a label map by upsampling or resampling a multi-class one-hot encoded image (such as a softmax model prediction) to the space of a binary image (such as a sigmoid model prediction). More...
class	LinearIntensityMappingOperation
	Apply a linear shift and scale to the image intensities. More...
class	MRIBiasFieldCorrectionOperation
	Operation to perform bias field correction using an implicitly trained neural network (see MRIBiasFieldCorrectionAlgorithm for more details and the parameters description) More...
class	MRIBiasFieldGenerationOperation
	Generate and optionally apply a smooth multiplicative intensity modulation ("bias") field. More...
class	MakeFloatOperation
	Turn image into a float image (if not float already) More...
class	TagDataElementOperation
	Operation for changing data element tags. More...
class	MarkAsTargetOperation
	Mark elements from the input data item as "target" which might affect the behavior of subsequent operations that rely on Operation::ProcessingPolicy or use other custom target-specific logic. More...
class	UnmarkAsTargetOperation
	Remove the target tag from the elements of the input data item. More...
class	MergeAsChannelsOperation
	Merge multiple images into one along the channel dimension. More...
class	MorphologicalFilterOperation
	Runs a morphological operation on the input mode (string): Name of the operation in ['dilation', 'erosion', 'opening', 'closing'] op_size (int): Size of the structuring element. More...
class	ConcatenateNeighboringFramesToChannelsOperation
	Iterates over frame and adds to channel dimension the neighboring frames of both sides of the frame. More...
class	NormalizeMADOperation
	MAD (median absolute deviation) Normalize Operation. More...
class	NormalizeNormalOperation
	Channel-wise normalize values to mean 0, std 1, ignoring a certain background value if needed. More...
class	NormalizePercentileOperation
	Normalize the input image based on its intensity distribution, in particular on a lower and upper percentile. More...
class	NormalizeUniformOperation
	Normalize values in range [a, b]. More...
class	OneHotOperation
	Transform a label map into a multi-channel image based on a one-hot encoding Up to 4 channels are supported with OpenGL, more channels will fall back to CPU. More...
class	PadOperation
	Pad an image to a specific padding size in each dimension. More...
class	PadDimsOperation
	Pad an image to specific target dimensions. More...
class	PadDimsToNextMultipleOperation
	Pads each dimension of the input image to the next multiple of the specified divisor. More...
class	PolyCropOperation
	Masks the image with a convex polygon as described in Markova et al. More...
class	RandomAddDegradedLabelAsChannelOperation
	Operation to add a channel with randomly distributed blobs, whose sign is positive if a blob is in the label and else negative. More...
class	RandomAddRandomNoiseOperation
	Operation that randomly varies the intensity strength of the AddRandomNoiseOperation. More...
class	RandomAxisFlipOperation
	Flip image content along specified set of axes, with independent sampling for each axis. More...
class	RandomAxisRotationOperation
	Rotate around image axis with axis-specific rotation angles that are signed multiples of 90 degrees. More...
class	RandomChoiceOperation
	Meta-operation that picks one operation from its configuration randomly and executes it This is particularly useful for image samplers, where we might want to alternate between different ways of sampling the input images The operationWeights argument allows to parameterize the operation selection probability distribution, if not specified, uniform sampling is used. More...
class	RandomCropAroundLabelMapOperation
	Random version of CropAroundLabelMapOperation that selects a single random label value and crops around it. More...
class	RandomCropOperation
	Crop input images and label maps with a random factor crop_ranges (vec3): List of floats from [0;1] specifying the maximum percentage of the dimension to crop, for each axis. More...
class	RandomCutOutOperation
	Cut out regions in input images and label maps with a random factor cutout_number_range (vec2i): List of integers specifying the minimum and maximum number of cutout regions cutout_value_range (vec2f): List of floats specifying the minimum and maximum fill value for cutout regions cutout_size_lower (vec3): List of floats specifying the lower bound of the cutout region size for each dimension cutout_size_upper (vec3): List of floats specifying the upper bound of the cutout region size for each dimension cutout_size_units (ParamUnit): Units of the cutout size bounds, Default: ParamUnit::MM. More...
class	RandomDeformationOperation
	Same as DeformationOperation but samples displacements randomly from a specified range nSubdivisions (vec3i): list specifying the number of subdivisions for each dimension (the number of control points is subdivisions+1) maxAbsDisplacement (float): absolute value of the maximum possible displacement (mm) paddingMode (PaddingMode): defines which type of padding is used. More...
class	RandomGammaCorrectionOperation
	Apply a random gamma correction which changes the overall contrast (see https://en.wikipedia.org/wiki/Gamma_correction). More...
class	RandomImageFromLabelOperation
	Creates a random image from a label map, each label is sampled from a Gaussian distribution. More...
class	RandomInvertOperation
	Operation that randomly inverts an image with a default probability of 50% (can be changed) More...
class	RandomKeypointJitterOperation
	Adds an individually and randomly sampled offset to each keypoint of each KeypointElement. More...
class	RandomLinearIntensityMappingOperation
	Apply a random affine intensity mapping to an image. More...
class	RandomMRIBiasFieldGenerationOperation
	Apply a random multiplicative bias field The field amplitude, length scale and distance scaling are drawn from uniform distributions. More...
class	RandomPolyCropOperation
	Masks the image with a random convex polygon as described in Markova et al. More...
class	RandomResolutionReductionOperation
	Reduces the resolution of an image to a spacing randomly sampled in each dimension between the image spacing and the specified max_spacing max_spacing (vec3): maximum spacing for resolution reduction. More...
class	RandomRotationOperation
	Rotate input images and label maps with random angles. More...
class	RandomScalingOperation
	Scale input images and label maps with random factors scales_range (vec3): List of floats specifying the upper bound of the range from which the scaling ofset will be sampled. More...
class	RandomSmoothOperation
	Apply a random smoothing on the image (Gaussian kernel). More...
class	RandomTemplateInpaintingOperation
	Inpaints a template into an image with randomly selected spatial and intensity transformation in a given range. More...
class	RectifyRotationOperation
	Sets the rotation matrix of each element to the nearest xyz-axis aligned rotation to avoid oblique angles when baking in the rotation. More...
class	RemoveOperation
	Remove a set of fields from a DataItem Use 'apply_to' from base to specify which fields to remove. More...
class	RemoveMaskOperation
	Removes the mask of all input images. More...
class	RenameOperation
	Rename a set of fields of a DataItem source (List[str]): list of the elements to be replaced target (List[str]): list of names of the new elements (must match the size of source) throw_error_on_missing_source (bool): if source field is missing, then throw an error (otherwise do nothing) throw_error_on_existing_target (bool): if target field already exists, then throw an error (otherwise overwrite it) More...
class	ReplaceLabelsValuesOperation
	Replace label values (assumes that it is unsigned byte) More...
class	ResampleDimsOperation
	Resample input to target dimensions. More...
class	ResampleKeepingAspectRatioOperation
	Resample input to target dimensions while keeping aspect ratio of original images. More...
class	ResampleOperation
	Resample input to target spacing. More...
class	ResampleToInputOperation
	Resample to a target image. More...
class	ResolutionReductionOperation
	Reduces the resolution of an image to a specified spacing by keeping image dimensions target_spacing (vec3): target spacing for intermediate downsampling before upsampling again. More...
class	RotationOperation
	Rotate input images and label maps with fixed angles. More...
class	RunModelOperation
	Run a machine learning model on the input item and merge the prediction to the input item. More...
class	ScalingOperation
	Scale input images and label maps with fixed factors scales (vec3): Scaling factor applied to each dimension apply_now (bool): Bake transformation right way (otherwise, just changes the matrix) More...
class	SelectChannelsOperation
	Select a sub-set of the input channels. More...
class	SetModalityOperation
	Sets the data modality. More...
class	SetLabelModalityOperation
	Sets the data modality of labels to Data::Modality::LABEL if data type is PixelType::UByte, otherwise casts a warning and skips execution. More...
class	SetMatrixToIdentityOperation
	Set the matrices of all images to identity (associated landmarks and boxes will be moved accordingly). More...
class	SetSpacingOperation
	Sets spacing of image elements (data buffer is not changed). More...
class	SigmoidOperation
	Apply a sigmoid function on values. More...
class	SmoothOperation
	Run a convolution with a Gaussian kernel on the input image. More...
class	SoftmaxOperation
	Computes channel-wise softmax of input image. More...
class	SplitIntoPatchesOperation
	Operation which splits the input image into overlapping patches for sliding window inference. More...
class	StandardizeImageAxesOperation
	Reorganize the memory buffer of a medical image to ensure anatomical consistency. More...
class	SwapImageAndLabelsOperation
	Swap image and labels. More...
class	SyncOperation
	Sync shared memory of images. More...
class	TanhOperation
	Apply a tanh function on values. More...
class	TemplateInpaintingOperation
	Inpaints a template into an image with specified spatial and intensity transformation. More...
class	ThresholdOperation
	Threshold values of the input image. More...
class	UndoPaddingOperation
	Apply the inverse of a previously applied padding operation. More...