com.emphysic.myriad.core.data.roi

Class ExternalROIFinder

java.lang.Object

com.emphysic.myriad.core.data.roi.ExternalROIFinder

All Implemented Interfaces:

ROIFinder, ObjectMap, com.esotericsoftware.kryo.KryoSerializable

public class ExternalROIFinder
extends java.lang.Object
implements ROIFinder

ExternalROIFinder - demonstrates one way to call external ROI applications by redirecting their standard input and output streams.

Constructor Summary

Constructors

Constructor and Description
ExternalROIFinder() Constructor for an empty ROIFinder (serialization)
ExternalROIFinder(ExternalProcess externalProcess) Creates a new ExternalROIFinder with the specified external process manager.

Method Summary

Modifier and Type	Method and Description
static ExternalROIFinder	buildROIFinder(java.lang.String cmd) Convenience method for building an external ROI finder
static ExternalROIFinder	buildROIFinder(java.lang.String cmd, java.util.List<java.lang.String> args) Convenience method for building an external ROI finder
static ExternalROIFinder	buildROIFinder(java.lang.String cmd, java.util.List<java.lang.String> args, java.io.File workingFolder) Convenience method for building an external ROI finder
static ExternalROIFinder	buildROIFinder(java.lang.String cmd, java.util.List<java.lang.String> args, java.util.Map<java.lang.String,java.lang.String> environment, java.io.File workingFolder) Convenience method for building an external ROI finder
java.util.Map<java.lang.String,java.lang.Object>	getObjectMap() Creates a map of the important fields for the instance, suitable for serialization.
ExternalProcess	getProcessRunner() Returns the external application for this ROIFinder
long	getSerializationVersion() Returns the current version of the serialization format.
long	getTimeout() Returns the number of seconds, milliseconds, etc.
java.util.concurrent.TimeUnit	getTimeoutUnits() Returns the units of the timeout delay.
int	getVersion() Returns the current class version.
void	initCurrentVersion(java.util.Map<java.lang.String,java.lang.Object> objectMap) Initializes an instance with a current-version object graph.
(package private) boolean	isLogMessage(java.lang.String input) Determines whether the specified message appears to be a logging message, i.e.
(package private) boolean	isMyriadMessage(java.lang.String input) Determines whether the specified message appears to be directed to Myriad, i.e.
boolean	isROI(Dataset dataset) Predict whether the specified sample appears to contain a region of interest.
boolean	isROI(double[] data) Starts external application and has it classify data as from a flaw or not.
(package private) boolean	isROIMessage(java.lang.String input) Determines whether the specified message appears to be a Region Of Interest determination, i.e.
void	legacyRead(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Input input)
void	legacyWrite(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Output output)
(package private) boolean	ROIfound(java.lang.String input) Determines whether the specified message indicates a Region of Interest was found by the external ROI finder.
void	setProcessRunner(ExternalProcess processRunner) Sets the external application for this ROIFinder
void	setTimeout(long timeout, java.util.concurrent.TimeUnit timeoutUnits) Sets the external process timeout.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface com.emphysic.myriad.core.data.roi.ROIFinder

fromFile

Methods inherited from interface com.emphysic.myriad.core.data.util.ObjectMap

init, initPreviousVersion, initUnknownVersion, load, read, save, write

Constructor Detail

ExternalROIFinder

public ExternalROIFinder()

Constructor for an empty ROIFinder (serialization)

ExternalROIFinder

public ExternalROIFinder(ExternalProcess externalProcess)

Creates a new ExternalROIFinder with the specified external process manager.

Parameters:

externalProcess - external process manager

Method Detail

isROI

public boolean isROI(double[] data)

Starts external application and has it classify data as from a flaw or not. Data are passed as space-delimited numbers to the app's standard input; the external application reports whether a flaw was found or not by printing a line "myriad:T" to its standard output.

In a "real" deployment the external app would likely run indefinitely, would communicate over a network connection, etc.

Specified by:

isROI in interface ROIFinder

Parameters:

data - raw data to examine

Returns:

true if the app found a flaw, false if not or if an error occurred

See Also:

for information on setting the timeout delay

isMyriadMessage

boolean isMyriadMessage(java.lang.String input)

Determines whether the specified message appears to be directed to Myriad, i.e. starts with "Myriad:".

Parameters:

input - message to check

Returns:

true if the message matches the regex ^Myriad (case insensitive).

isLogMessage

boolean isLogMessage(java.lang.String input)

Determines whether the specified message appears to be a logging message, i.e. a Myriad message with one of DEBUG, INFO, WARN, or ERROR (case insensitive) defined.

Parameters:

input - message to check

Returns:

true if the message matches the regex ^Myriad (case insensitive).

isROIMessage

boolean isROIMessage(java.lang.String input)

Determines whether the specified message appears to be a Region Of Interest determination, i.e. starts with "Myriad:" and has one of TRUE or FALSE (case insensitive).

Parameters:

input - message to check

Returns:

true if the message appears to be an ROI call

ROIfound

boolean ROIfound(java.lang.String input)

Determines whether the specified message indicates a Region of Interest was found by the external ROI finder.

Parameters:

input - message to check

Returns:

true if the external ROI finder found an ROI, false if not or if the message was invalid

getTimeout

public long getTimeout()

Returns the number of seconds, milliseconds, etc. before the external process times out.

Returns:

value of timeout

See Also:

getTimeoutUnits()

getTimeoutUnits

public java.util.concurrent.TimeUnit getTimeoutUnits()

Returns the units of the timeout delay.

Returns:

timeout units

See Also:

getTimeout()

setTimeout

public void setTimeout(long timeout,
                       java.util.concurrent.TimeUnit timeoutUnits)

Sets the external process timeout. Defaults to 10 seconds.

Parameters:

timeout - amount of time

timeoutUnits - units of time

isROI

public boolean isROI(Dataset dataset)

Predict whether the specified sample appears to contain a region of interest.

Specified by:

isROI in interface ROIFinder

Parameters:

dataset - data to examine

Returns:

true if the sample appears to contain an ROI, false otherwise

getSerializationVersion

public long getSerializationVersion()

Description copied from interface: ObjectMap

Returns the current version of the serialization format. Increments when the serialization format changes, i.e. backwards compatibility is broken.

Specified by:

getSerializationVersion in interface ObjectMap

Returns:

serialization version

getVersion

public int getVersion()

Description copied from interface: ObjectMap

Returns the current class version. Class version increments when the class changes but doesn't necessarily break compatibility with serialization.

Specified by:

getVersion in interface ObjectMap

Returns:

class version

getObjectMap

public java.util.Map<java.lang.String,java.lang.Object> getObjectMap()

Description copied from interface: ObjectMap

Creates a map of the important fields for the instance, suitable for serialization.

Specified by:

getObjectMap in interface ObjectMap

Returns:

"object map" of the instance

initCurrentVersion

public void initCurrentVersion(java.util.Map<java.lang.String,java.lang.Object> objectMap)

Description copied from interface: ObjectMap

Initializes an instance with a current-version object graph.

Specified by:

initCurrentVersion in interface ObjectMap

Parameters:

objectMap - object graph for initialization

buildROIFinder

public static ExternalROIFinder buildROIFinder(java.lang.String cmd,
                                               java.util.List<java.lang.String> args,
                                               java.io.File workingFolder)

Convenience method for building an external ROI finder

Parameters:

cmd - full path and filename of the application to execute

args - list of command-line arguments to provide the application

workingFolder - the working folder for the application

Returns:

an ROI finder that calls the specified application to classify data

buildROIFinder

public static ExternalROIFinder buildROIFinder(java.lang.String cmd,
                                               java.util.List<java.lang.String> args)

Convenience method for building an external ROI finder

Parameters:

cmd - full path and filename of the application to execute

args - list of command-line arguments to provide the application

Returns:

an ROI finder that calls the specified application to classify data

buildROIFinder

public static ExternalROIFinder buildROIFinder(java.lang.String cmd)

Convenience method for building an external ROI finder

Parameters:

cmd - full path and filename of the application to execute

Returns:

an ROI finder that calls the specified application to classify data

buildROIFinder

public static ExternalROIFinder buildROIFinder(java.lang.String cmd,
                                               java.util.List<java.lang.String> args,
                                               java.util.Map<java.lang.String,java.lang.String> environment,
                                               java.io.File workingFolder)

Convenience method for building an external ROI finder

Parameters:

cmd - full path and filename of the application to execute

args - list of command-line arguments to provide the application

environment - environment variables for the application, or null to use the current system environment

workingFolder - the working folder for the application, or null for "user.dir" working folder

Returns:

an ROI finder that calls the specified application to classify data

legacyWrite

public void legacyWrite(com.esotericsoftware.kryo.Kryo kryo,
                        com.esotericsoftware.kryo.io.Output output)

legacyRead

public void legacyRead(com.esotericsoftware.kryo.Kryo kryo,
                       com.esotericsoftware.kryo.io.Input input)

getProcessRunner

public ExternalProcess getProcessRunner()

Returns the external application for this ROIFinder

Returns:

external application

setProcessRunner

public void setProcessRunner(ExternalProcess processRunner)

Sets the external application for this ROIFinder

Parameters:

processRunner - external application