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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
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