A B C D E F G H I K L M N O P R S T U V W X Y

S

safeIdx(int, int) - Static method in class com.emphysic.myriad.core.data.util.DatasetUtils

Safe handling of out of bound index requests - returns index requested if 0 < value < endIndex, 0 if value < 0, endIndex - 1 otherwise

samples - Variable in class com.emphysic.myriad.core.ml.CrossValidation.Data

save(File) - Method in interface com.emphysic.myriad.core.data.util.ObjectMap

Saves a model to disk

saveCredentials() - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

Reports the current basic auth serialization settings.

ScalingOperation - Class in com.emphysic.myriad.core.data.ops

ScalingOperation - scales a Dataset by substracting its mean and dividing by the standard deviation.

ScalingOperation(double, double) - Constructor for class com.emphysic.myriad.core.data.ops.ScalingOperation

Creates a new ScalingOperation with the specified mean and standard deviation.

ScalingOperation() - Constructor for class com.emphysic.myriad.core.data.ops.ScalingOperation

Initializes a new ScalingOperation.

scharr(Dataset) - Static method in class com.emphysic.myriad.core.examples.EdgeDetection

Performs Scharr edge detection on a dataset https://en.wikipedia.org/wiki/Sobel_operator#Alternative_operators

ScharrOperation - Class in com.emphysic.myriad.core.data.ops

ScharrOperation - variation of the Sobel operator, an optimization minimizing weighted mean squared angular error in the Fourier domain.

ScharrOperation() - Constructor for class com.emphysic.myriad.core.data.ops.ScharrOperation

Creates a new ScharrOperation

secondBlur - Variable in class com.emphysic.myriad.core.data.ops.DifferenceOfGaussiansOperation

Second blur operation

set(int, int, double) - Method in class com.emphysic.myriad.core.data.io.Dataset

Sets the value of a point.

setArgs(List<String>) - Method in class com.emphysic.myriad.core.data.util.ExternalProcess

Sets the command line arguments.

setAutoThreshold(CannyOperation.AutoThreshold) - Method in class com.emphysic.myriad.core.data.ops.CannyOperation

Sets the auto thresholding

setBigFileSize(long) - Method in class com.emphysic.myriad.core.data.io.ImageDataset

Sets the threshold size in bytes for "big" images.

setBlockSize(int) - Method in class com.emphysic.myriad.core.data.ops.HOGOperation

setBlur(BlurOperation) - Method in class com.emphysic.myriad.core.data.ops.GaussianPyramidOperation

setBlurOperation(BlurOperation) - Method in class com.emphysic.myriad.core.data.ops.CannyOperation

Sets the operation used to denoise data prior to edge detection.

setCellRadius(int) - Method in class com.emphysic.myriad.core.data.ops.HOGOperation

setCellWidth(int) - Method in class com.emphysic.myriad.core.data.ops.HOGOperation

setCmd(String) - Method in class com.emphysic.myriad.core.data.util.ExternalProcess

Sets the command to execute.

setCommentChar(String) - Method in class com.emphysic.myriad.core.data.io.TextDataset

Sets the comment character.

setConfidenceThreshold(double) - Method in class com.emphysic.myriad.core.data.roi.MLROIConfFinder

Sets the confidence threshold for labelling ROI samples - the model must be (confThr * 100)% confident a sample contains ROI for it to be labelled as such.

setConnectionTimeout(long) - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

setCurrentMean(double) - Method in class com.emphysic.myriad.core.data.ops.math.OnlineStats

setData(Dataset) - Method in class com.emphysic.myriad.core.data.io.Dataset

Sets this Dataset's data to a copy of the specified's data.

setData(double[], int, int) - Method in class com.emphysic.myriad.core.data.io.Dataset

Sets this Dataset's data to a copy of the specified data.

setDelim(String) - Method in class com.emphysic.myriad.core.data.io.TextDataset

Sets the token delimiter.

setEnv(Map<String, String>) - Method in class com.emphysic.myriad.core.data.util.ExternalProcess

Sets the environment for the external process.

setExhaustive(boolean) - Method in class com.emphysic.myriad.core.data.util.FileSniffer

Sets whether to perform exhaustive matching or not.

setFeatureMeans(List<Double>) - Method in class com.emphysic.myriad.core.data.ops.FeatureScalingOperation

Sets the feature means

setFeatureStds(List<Double>) - Method in class com.emphysic.myriad.core.data.ops.FeatureScalingOperation

Sets the feature standard deviations

setFinder(ROIFinder) - Method in class com.emphysic.myriad.core.data.roi.ROIBundle

setGradientOperation(SobelOperation) - Method in class com.emphysic.myriad.core.data.ops.CannyOperation

Sets the operation used to calculate horizontal and vertical gradients

setH(int) - Method in class com.emphysic.myriad.core.experimental.aparapi.kernels.ConvolutionKernel

setHeader(Map<String, String>) - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

sethKernel(double[][]) - Method in class com.emphysic.myriad.core.data.ops.math.GradientVector

Sets the kernel for calculating horizontal gradient

setHttpClient(HttpClient) - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

Sets the HTTPClient implementation to use.

setIdata(double[]) - Method in class com.emphysic.myriad.core.experimental.aparapi.kernels.ConvolutionKernel

setKnl(double[][]) - Method in class com.emphysic.myriad.core.experimental.aparapi.kernels.ConvolutionKernel

setLearner(Learner) - Method in class com.emphysic.myriad.core.data.roi.SGDROIFinder

Sets the model trainer.

setLearningRate(double) - Method in class com.emphysic.myriad.core.data.roi.PassiveAggressiveROIFinder

Sets the learning rate.

setLinearModel(Model) - Method in class com.emphysic.myriad.core.data.roi.SGDROIFinder

Sets the SGD model

setLowerThreshold(double) - Method in class com.emphysic.myriad.core.data.ops.CannyOperation

Sets the "weak" or lower threshold for edge detection - elements with values greater than or equal to this value are considered edges.

setMAXANGLE(double) - Method in class com.emphysic.myriad.core.data.ops.HOGOperation

Sets the maximum angle in the histogram in radians.

setMean(double) - Method in class com.emphysic.myriad.core.data.ops.ScalingOperation

Sets the mean value used in normalization.

setMetadata(String) - Method in class com.emphysic.myriad.core.data.roi.ROI

Sets the descriptive metadata for this ROI

setMetadata(Map<String, String>) - Method in class com.emphysic.myriad.core.data.roi.ROIBundle

setMetadataEntry(String, String) - Method in class com.emphysic.myriad.core.data.roi.ROIBundle

setMINANGLE(double) - Method in class com.emphysic.myriad.core.data.ops.HOGOperation

Sets the minimum angle in the histogram in radians.

setModel(AdaptiveLogisticRegression) - Method in class com.emphysic.myriad.core.data.roi.AdaptiveSGDROIFinder

Sets the current meta-model

setModel(PassiveAggressive) - Method in class com.emphysic.myriad.core.data.roi.PassiveAggressiveROIFinder

Sets the ROI model.

setModel(GradientMachine) - Method in class com.emphysic.myriad.core.experimental.roi.GradMachineROIFinder

setN(int) - Method in class com.emphysic.myriad.core.data.ops.math.OnlineStats

setNbins(int) - Method in class com.emphysic.myriad.core.data.ops.HOGOperation

Sets the number of bins to use in the histogram

setNext(ActorRef) - Method in class com.emphysic.myriad.network.LinkedWorkerPool

Sets the next link in the chain

setNumCategories(int) - Method in class com.emphysic.myriad.core.data.roi.AdaptiveSGDROIFinder

Sets the number of categories for this model.

setNumCategories(int) - Method in class com.emphysic.myriad.core.data.roi.PassiveAggressiveROIFinder

Sets the number of categories for the model.

setNumFeatures(int) - Method in class com.emphysic.myriad.core.data.roi.AdaptiveSGDROIFinder

Sets the number of features for this model.

setNumFeatures(int) - Method in class com.emphysic.myriad.core.data.roi.PassiveAggressiveROIFinder

Sets the number of features in the sample data.

setOdata(double[]) - Method in class com.emphysic.myriad.core.experimental.aparapi.kernels.ConvolutionKernel

setOperation(DatasetOperation) - Method in class com.emphysic.myriad.network.DatasetActor

Sets the operation to perform on each Dataset

setOrigin(int, int...) - Method in class com.emphysic.myriad.core.data.roi.ROI

Sets the bounding box origin for the ROI.

setPassword(String) - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

setPoolSize(int) - Method in class com.emphysic.myriad.core.data.roi.AdaptiveSGDROIFinder

Sets the number of SGD learners in the meta-model.

setPreproc(DatasetOperation) - Method in class com.emphysic.myriad.core.data.roi.ROIBundle

setPriorFunction(PriorFunction) - Method in class com.emphysic.myriad.core.data.roi.AdaptiveSGDROIFinder

Sets the regularization function used to limit overfitting.

setProcessRunner(ExternalProcess) - Method in class com.emphysic.myriad.core.data.roi.ExternalROIFinder

Sets the external application for this ROIFinder

setRadius(int) - Method in class com.emphysic.myriad.core.data.ops.BlurOperation

Sets the blur radius.

setRouter(ActorRef) - Method in class com.emphysic.myriad.network.WorkerPool

Sets the worker manager

setSaveCredentials(boolean) - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

Sets whether or not to save basic auth credentials during serialization.

setScaleFactor(int) - Method in class com.emphysic.myriad.core.data.ops.GaussianPyramidOperation

Decimation factor - typically 2 to make each level of the pyramid 1/2 the size of its predecessor.

setSigmaThreshold(double) - Method in class com.emphysic.myriad.core.data.ops.CannyOperation

Sets the threshold parameter for auto-thresholding based on the mean or median

setSocketTimeout(long) - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

setStd(double) - Method in class com.emphysic.myriad.core.data.ops.ScalingOperation

Sets the standard deviation used in normalization.

setSumSquaredMeanDiff(double) - Method in class com.emphysic.myriad.core.data.ops.math.OnlineStats

setThreadCount(int) - Method in class com.emphysic.myriad.core.data.roi.AdaptiveSGDROIFinder

Sets the number of threads to use during training.

setThreshold(double) - Method in class com.emphysic.myriad.core.data.ops.BinarizeOperation

Threshold for binarization

setTimeout(long, TimeUnit) - Method in class com.emphysic.myriad.core.data.roi.ExternalROIFinder

Sets the external process timeout.

setUpperThreshold(double) - Method in class com.emphysic.myriad.core.data.ops.CannyOperation

Sets the "strong" or upper threshold for edge detection - elements with values greater than or equal to this value are considered edges.

setUrl(String) - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

setUsername(String) - Method in class com.emphysic.myriad.core.data.roi.RESTROIFinder

setvKernel(double[][]) - Method in class com.emphysic.myriad.core.data.ops.math.GradientVector

Sets the kernel for calculating vertical gradient

setW(int) - Method in class com.emphysic.myriad.core.experimental.aparapi.kernels.ConvolutionKernel

setWindowSize(int) - Method in class com.emphysic.myriad.core.data.ops.GaussianPyramidOperation

Sets the cutoff size of the pyramid - operation is complete when this threshold is reached

setWorkingFolder(File) - Method in class com.emphysic.myriad.core.data.util.ExternalProcess

Sets the working folder for the external process.

SGDROIFinder - Class in com.emphysic.myriad.core.data.roi

SGDROIFinder - machine learning region of interest detection based on the Stochastic Gradient Descent (SGD) algorithm.

SGDROIFinder() - Constructor for class com.emphysic.myriad.core.data.roi.SGDROIFinder

Creates a new SGD ROI finder using the Hinge loss function and a regularization set to 1.0E-5.

SGDROIFinder(Loss, double) - Constructor for class com.emphysic.myriad.core.data.roi.SGDROIFinder

Creates a new SGD ROI finder using the specified loss function and regularization.

SGDROIFinder(Model) - Constructor for class com.emphysic.myriad.core.data.roi.SGDROIFinder

Instantiates a new SGD ROI finder from an existing SGD model.

shutdown() - Method in class com.emphysic.myriad.network.LinkedWorkerPool

Initiates shutdown procedure.

shutdown() - Method in class com.emphysic.myriad.network.WorkerPool

Initiates shutdown

ShutdownMessage - Class in com.emphysic.myriad.network.messages

ShutdownMessage - informs the Myriad components that a shutdown has been requested

ShutdownMessage(String) - Constructor for class com.emphysic.myriad.network.messages.ShutdownMessage

ShutdownMessage() - Constructor for class com.emphysic.myriad.network.messages.ShutdownMessage

SlidingWindow - Class in com.emphysic.myriad.core.examples

Demonstrates use of the "sliding window" algorithm to examine small subsets of a larger Dataset.

SlidingWindow() - Constructor for class com.emphysic.myriad.core.examples.SlidingWindow

SlidingWindowActor - Class in com.emphysic.myriad.network

SlidingWindowActor - performs sliding window operation on Datasets.

SlidingWindowActor(int, int, int, DatasetOperation) - Constructor for class com.emphysic.myriad.network.SlidingWindowActor

Creates a new rectangular sliding window actor

SlidingWindowActor(int, int, DatasetOperation) - Constructor for class com.emphysic.myriad.network.SlidingWindowActor

Creates a new sliding window actor

SlidingWindowActor(int, int) - Constructor for class com.emphysic.myriad.network.SlidingWindowActor

Creates a new sliding window actor with no operation performed on the window.

SlidingWindowOperation - Class in com.emphysic.myriad.core.data.ops

SlidingWindowOperation - moves a "window" across a Dataset.

SlidingWindowOperation(int, int, int, DatasetOperation) - Constructor for class com.emphysic.myriad.core.data.ops.SlidingWindowOperation

Creates a new SlidingWindowOperation.

SlidingWindowOperation(int, int, DatasetOperation) - Constructor for class com.emphysic.myriad.core.data.ops.SlidingWindowOperation

SlidingWindowOperation(int, int, int) - Constructor for class com.emphysic.myriad.core.data.ops.SlidingWindowOperation

SlidingWindowOperation(int, int) - Constructor for class com.emphysic.myriad.core.data.ops.SlidingWindowOperation

Creates a new SlidingWindowOperation.

SlidingWindowOperation() - Constructor for class com.emphysic.myriad.core.data.ops.SlidingWindowOperation

Creates a new SlidingWindowOperation with a 5x5 window and stepsize 5.

SlidingWindowPool - Class in com.emphysic.myriad.network

SlidingWindowPool - a linked worker pool performing sliding windows.

SlidingWindowPool(int, int, int, int, DatasetOperation) - Constructor for class com.emphysic.myriad.network.SlidingWindowPool

Creates a new pool

SlidingWindowPool(int, int, int, int) - Constructor for class com.emphysic.myriad.network.SlidingWindowPool

Creates a new pool

SlidingWindowPool(int, int, int, DatasetOperation) - Constructor for class com.emphysic.myriad.network.SlidingWindowPool

Creates a new pool

SlidingWindowPool(int, int, DatasetOperation) - Constructor for class com.emphysic.myriad.network.SlidingWindowPool

Creates a new pool

SlidingWindowPool(int, int, int) - Constructor for class com.emphysic.myriad.network.SlidingWindowPool

Creates a new pool with no DatasetOperation performed on each window.

SlidingWindowPool(int, int) - Constructor for class com.emphysic.myriad.network.SlidingWindowPool

Creates a new pool

sniff(File) - Method in class com.emphysic.myriad.core.data.util.FileSniffer

Attempts to automatically return a Dataset from a supported file format.

sniff(File) - Method in interface com.emphysic.myriad.core.data.util.Sniffer

Attempts to read an input file automatically

sniff(File) - Method in class com.emphysic.myriad.core.data.util.TextSniffer

Examines the specified file and attempts to automatically create a Dataset from the contents.

Sniffer - Interface in com.emphysic.myriad.core.data.util

Sniffer - an interface for attempting to automatically read an input file

sobel(Dataset) - Static method in class com.emphysic.myriad.core.examples.EdgeDetection

Performs Sobel edge detection on a dataset https://en.wikipedia.org/wiki/Sobel_operator

SobelOperation - Class in com.emphysic.myriad.core.data.ops

SobelOperation - applies the Sobel operator to an input.

SobelOperation() - Constructor for class com.emphysic.myriad.core.data.ops.SobelOperation

Creates a new SobelOperation.

source - Variable in class com.emphysic.myriad.core.data.io.IODataset

Source of the data

start() - Method in class com.emphysic.myriad.core.data.util.ExternalProcess

Starts the external process

start(Pool, Class<? extends UntypedActor>, Object...) - Method in class com.emphysic.myriad.network.WorkerPool

Creates a new pool of workers

start(int, Class<? extends UntypedActor>, Object...) - Method in class com.emphysic.myriad.network.WorkerPool

Creates a new worker pool that tries to send to the non-suspended routee with fewest messages in mailbox.

start(Class<? extends UntypedActor>, Object...) - Method in class com.emphysic.myriad.network.WorkerPool

Creates a new worker pool that tries to send to the non-suspended routee with fewest messages in mailbox.

Stats - Class in com.emphysic.myriad.core.data.ops.math

Stats - general purpose statistical functions.

Stats() - Constructor for class com.emphysic.myriad.core.data.ops.math.Stats

stddev() - Method in class com.emphysic.myriad.core.data.ops.math.OnlineStats

Returns the current approximation of the standard deviation of the data.

stddev(double[]) - Method in class com.emphysic.myriad.core.data.ops.math.OnlineStats

Updates the statistics then returns the current standard deviation.

stddev(Dataset) - Method in class com.emphysic.myriad.core.data.ops.math.OnlineStats

Updates the statistics with the supplied values then returns the current standard deviation.

stddev(double[]) - Static method in class com.emphysic.myriad.core.data.ops.math.Stats

Calculates the standard deviation of the data

stddev(Dataset) - Static method in class com.emphysic.myriad.core.data.ops.math.Stats

Calculates the standard deviation of the data

SVMROIFinder - Class in com.emphysic.myriad.core.data.roi

SVMROIFinder - a Region Of Interest (ROI) finder based on an online Support Vector Machine (SVM).

SVMROIFinder(MercerKernel<double[]>, double, double) - Constructor for class com.emphysic.myriad.core.data.roi.SVMROIFinder

Constructor.

SVMROIFinder(MercerKernel<double[]>, double) - Constructor for class com.emphysic.myriad.core.data.roi.SVMROIFinder

Constructor.

SVMROIFinder(double, double) - Constructor for class com.emphysic.myriad.core.data.roi.SVMROIFinder

Constructor for a linear kernel SVM.

SVMROIFinder(double) - Constructor for class com.emphysic.myriad.core.data.roi.SVMROIFinder

Constructor for a linear kernel SVM.

SVMROIFinder() - Constructor for class com.emphysic.myriad.core.data.roi.SVMROIFinder

Default constructor.

SVMROIFinder(SVM) - Constructor for class com.emphysic.myriad.core.data.roi.SVMROIFinder

Constructor

A B C D E F G H I K L M N O P R S T U V W X Y