org.youscope.plugin.lifecelldetection

Class CellDetectionJobConfiguration

java.lang.Object

org.youscope.common.job.JobConfiguration

org.youscope.plugin.lifecelldetection.CellDetectionJobConfiguration

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Configuration, JobContainerConfiguration, TableProducerConfiguration

public class CellDetectionJobConfiguration
extends JobConfiguration
implements TableProducerConfiguration, JobContainerConfiguration

This job takes an image an detects the cells therein.

Author:

Moritz Lang

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DETECTED_CELLS_IMAGE_SUFFIX The suffix added to the image save name to identify the detected cell image.
static java.lang.String	TYPE_IDENTIFIER The identifier for this measurement type.

Constructor Summary

Constructors

Constructor and Description
CellDetectionJobConfiguration()

Method Summary

Modifier and Type	Method and Description
void	addJob(JobConfiguration job) Adds a job to the job list.
void	addJob(JobConfiguration job, int index) Adds a job to the job list.
void	clearJobs() Removes all jobs from the job list.
CellDetectionJobConfiguration	clone()
java.lang.String	getCellTableSaveName() Returns the name under which the cell table should be saved (without extension).
java.lang.String	getControlImageSaveName() Returns the name under which the control image should be saved.
java.lang.String	getDescription() Returns a short description of this job.
CellDetectionConfiguration	getDetectionAlgorithmConfiguration() Return the configuration of the cell detection algorithm to use.
JobConfiguration	getDetectionJob() Returns the job which is used to produce the cell detection image.
JobConfiguration[]	getJobs() Returns the job list which might be edited by the caller.
long	getMinimalTimeMS() Returns the minimal time (in ms) the execution of the job should take.
TableDefinition	getProducedTableDefinition() Returns the definition of the table layout of the tables produced by this producer, e.g.
java.lang.String	getSegmentationImageSaveName() Returns the name under which the segmentation image should be saved.
java.lang.String	getTypeIdentifier() Returns a unique identifier for this configuration type.
CellVisualizationConfiguration	getVisualizationAlgorithmConfiguration() Returns the configuration of the cell visualization algorithm to use.
void	removeJobAt(int index) Removes the job at the given index.
void	setCellTableSaveName(java.lang.String name) Sets the name under which the cell-table should be saved.
void	setControlImageSaveName(java.lang.String name) Sets the name under which the control image should be saved.
void	setDetectionAlgorithmConfiguration(CellDetectionConfiguration detectionAlgorithmConfiguration) Sets the configuration of the cell detection algorithm to use.
void	setDetectionJob(JobConfiguration detectionJob) Sets the job which should be used to create the image which is used to detect the cells.
void	setJobs(JobConfiguration[] jobs) Sets the job list to the given list.
void	setMinimalTimeMS(long minimalTimeMS) Sets the minimal time (in ms) the execution of the job should take.
void	setSegmentationImageSaveName(java.lang.String name) Sets the name under which the segmentation image should be saved.
void	setVisualizationAlgorithmConfiguration(CellVisualizationConfiguration visualizationAlgorithmConfiguration) Set the configuration of the cell visualization algorithm to use.

Methods inherited from class org.youscope.common.job.JobConfiguration

checkConfiguration, toString

Methods inherited from class java.lang.Object

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

Field Detail

DETECTED_CELLS_IMAGE_SUFFIX

public static final java.lang.String DETECTED_CELLS_IMAGE_SUFFIX

The suffix added to the image save name to identify the detected cell image.

See Also:

Constant Field Values

TYPE_IDENTIFIER

public static final java.lang.String TYPE_IDENTIFIER

The identifier for this measurement type.

See Also:

Constant Field Values

Constructor Detail

CellDetectionJobConfiguration

public CellDetectionJobConfiguration()

Method Detail

getTypeIdentifier

public java.lang.String getTypeIdentifier()

Description copied from interface: Configuration

Returns a unique identifier for this configuration type. The identifier is used to determine factories and addons to construct and configure jobs, measurements, etc., given a corresponding configuration. Make sure that the ID returned is unique. The returned identifier should conform to "XXX.YYY", where XXX stands for an identifier of the organizational unit or the person who created the configuration (e.g. ETH, Smith, Cindarella), and YYY stands for an identifier of the specific kind of configuration (e.g. AutofocusJob, PlatePosition, MicroplateMeasurement). Optionally, additional hierarchy levels can be defined by additional separators ., e.g. "YouScope.AutofocusJob.Version1.1" The identifier should not contain spaces, non-ASCII characters, or colons (except for hierarchy level separation). Identifiers should start with a capital character, i.e. A-Z. Make sure to not use the same identifier for different configurations, since this might result in unexpected behavior or errors. Make

Specified by:

getTypeIdentifier in interface Configuration

Returns:

Unique identifier of the configuration type.

getJobs

public JobConfiguration[] getJobs()

Description copied from interface: JobContainerConfiguration

Returns the job list which might be edited by the caller.

Specified by:

getJobs in interface JobContainerConfiguration

Returns:

Job list.

setJobs

public void setJobs(JobConfiguration[] jobs)

Description copied from interface: JobContainerConfiguration

Sets the job list to the given list.

Specified by:

setJobs in interface JobContainerConfiguration

Parameters:

jobs - New job list.

addJob

public void addJob(JobConfiguration job)

Description copied from interface: JobContainerConfiguration

Adds a job to the job list.

Specified by:

addJob in interface JobContainerConfiguration

Parameters:

job - Job to be added.

clearJobs

public void clearJobs()

Description copied from interface: JobContainerConfiguration

Removes all jobs from the job list.

Specified by:

clearJobs in interface JobContainerConfiguration

removeJobAt

public void removeJobAt(int index)

Description copied from interface: JobContainerConfiguration

Removes the job at the given index.

Specified by:

removeJobAt in interface JobContainerConfiguration

Parameters:

index - Index of the job to be removed.

addJob

public void addJob(JobConfiguration job,
                   int index)

Description copied from interface: JobContainerConfiguration

Adds a job to the job list. The job is added such that it has the given index. Jobs having a higher or equal index before the operation are moved downwards.

Specified by:

addJob in interface JobContainerConfiguration

Parameters:

job - Job to be added.

index - Index where the job should be added.

getDetectionJob

public JobConfiguration getDetectionJob()

Returns the job which is used to produce the cell detection image. It is guaranteed that this job implements the ImageProducerConfigiguration interface.

Returns:

Image producing job for cell detection algorithm, or null.

setDetectionJob

public void setDetectionJob(JobConfiguration detectionJob)

Sets the job which should be used to create the image which is used to detect the cells. The job must implement the ImageProducerConfigiguration interface. If this is not given, the detection job is set to null.

Parameters:

detectionJob - Image producing job for cell detection algorithm, or null.

getControlImageSaveName

public java.lang.String getControlImageSaveName()

Returns the name under which the control image should be saved.

Returns:

name of image, or null, if image should not be saved.

setControlImageSaveName

public void setControlImageSaveName(java.lang.String name)

Sets the name under which the control image should be saved. Set to null to not save the image.

Parameters:

name - Name for the image, or null.

getSegmentationImageSaveName

public java.lang.String getSegmentationImageSaveName()

Returns the name under which the segmentation image should be saved.

Returns:

name of image, or null, if image should not be saved.

setSegmentationImageSaveName

public void setSegmentationImageSaveName(java.lang.String name)

Sets the name under which the segmentation image should be saved. Set to null to not save the image.

Parameters:

name - Name for the image, or null.

setCellTableSaveName

public void setCellTableSaveName(java.lang.String name)

Sets the name under which the cell-table should be saved. Set to null to not save the cell table.

Parameters:

name - Name for the cell table (without extension), or null.

getCellTableSaveName

public java.lang.String getCellTableSaveName()

Returns the name under which the cell table should be saved (without extension).

Returns:

name of cell-table, or null, if cell table should not be saved.

setDetectionAlgorithmConfiguration

public void setDetectionAlgorithmConfiguration(CellDetectionConfiguration detectionAlgorithmConfiguration)

Sets the configuration of the cell detection algorithm to use.

Parameters:

detectionAlgorithmConfiguration - Configuration of the algorithm.

getDetectionAlgorithmConfiguration

public CellDetectionConfiguration getDetectionAlgorithmConfiguration()

Return the configuration of the cell detection algorithm to use.

Returns:

Configuration of the algorithm.

getVisualizationAlgorithmConfiguration

public CellVisualizationConfiguration getVisualizationAlgorithmConfiguration()

Returns the configuration of the cell visualization algorithm to use. Returns null if not generating a cell detection visualization image.

Returns:

Cell visualization configuration, or null.

setVisualizationAlgorithmConfiguration

public void setVisualizationAlgorithmConfiguration(CellVisualizationConfiguration visualizationAlgorithmConfiguration)

Set the configuration of the cell visualization algorithm to use. Set to null to not generate a cell detection visualization image.

Parameters:

visualizationAlgorithmConfiguration - Cell visualization configuration, or null.

getDescription

public java.lang.String getDescription()

Description copied from class: JobConfiguration

Returns a short description of this job.

Specified by:

getDescription in class JobConfiguration

Returns:

Short description of the job.

clone

public CellDetectionJobConfiguration clone()

Overrides:

clone in class JobConfiguration

setMinimalTimeMS

public void setMinimalTimeMS(long minimalTimeMS)

Sets the minimal time (in ms) the execution of the job should take. If the execution of the job takes less, the rest of the time span will be waited. This function is mainly ment for real-time applications.

Parameters:

minimalTimeMS - The minimal time in ms the execution of the job has to take, or -1.

getMinimalTimeMS

public long getMinimalTimeMS()

Returns the minimal time (in ms) the execution of the job should take. If the execution of the job takes less, the rest of the time span will be waited. This function is mainly ment for real-time applications.

Returns:

The minimal time in ms the execution of the job has to take, or -1.

getProducedTableDefinition

public TableDefinition getProducedTableDefinition()

Description copied from interface: TableProducerConfiguration

Returns the definition of the table layout of the tables produced by this producer, e.g. the number and types of its columns. This function should return the same TableDefinition as is returned by a measurement component created by this configuration, see TableProducer.getProducedTableDefinition().

Specified by:

getProducedTableDefinition in interface TableProducerConfiguration

Returns:

Information about of the produced tables.