Package org.anchoranalysis.plugin.image.task.bean.format

Class ConvertImageFormat

Object

AnchorBean<Task<NamedChannelsInput,NoSharedState>>

Task<NamedChannelsInput,NoSharedState>

RasterTask<NoSharedState,OutputSequenceIndexed<Stack,String>>

ConvertImageFormat

public class ConvertImageFormat
extends RasterTask<NoSharedState,OutputSequenceIndexed<Stack,String>>

Converts each input-image to an output format, optionally changing the bit depth.

Stacks containing multiple series (i.e. multiple images in a single file) are supported.

If it looks like an RGB image, channels are written as a single RGB image. Otherwise, each channel is written separately.

If only a single stack will be converted, its name is suppressed in the output.

The following outputs are produced:

Output Name	Default?	Description
"converted"	yes	An image written in the default output format.
outputs from Task

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
ConvertImageFormat()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(NoSharedState sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
NoSharedState	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<NamedChannelsInput> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
protected OutputSequenceIndexed<Stack,String>	createSharedStateJob(InputOutputContext context)	Sets a new output-sequence for the series.
OutputEnabledMutable	defaultOutputs()	If specified, default rules for determine which outputs are enabled or not.
void	doStack(InputBound<NamedChannelsInput,NoSharedState> input, OutputSequenceIndexed<Stack,String> sharedStateJob, int seriesIndex, int numberSeries, InputOutputContext context)	Processes one stack from a series.
void	endSeries(NoSharedState sharedStateTask, OutputSequenceIndexed<Stack,String> sharedStateJob, InputOutputContext context)	Ends processing of a series.
ChannelConvertStyle	getChannelConversionStyle()	To convert as RGB or independently or in another way.
ConvertChannelTo<?>	getChannelConverter()	Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
boolean	hasVeryQuickPerInputExecution()	Is the execution-time of the task per-input expected to be very quick to execute?
boolean	isSuppressSeries()	If true, the series index is not included in the outputted file-names.
void	setChannelConversionStyle(ChannelConvertStyle channelConversionStyle)	To convert as RGB or independently or in another way.
void	setChannelConverter(ConvertChannelTo<?> channelConverter)	Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
void	setSuppressSeries(boolean suppressSeries)	If true, the series index is not included in the outputted file-names.
void	startSeries(NoSharedState sharedStateTask, OutputSequenceIndexed<Stack,String> sharedStateJob, InputOutputContext context)	Starts processing of a series.

Methods inherited from class org.anchoranalysis.plugin.image.task.bean.RasterTask

doJobOnInput, inputTypesExpected

Methods inherited from class org.anchoranalysis.experiment.bean.task.Task

executeJob, isInputCompatibleWith

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

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

Constructor Details

ConvertImageFormat

public ConvertImageFormat()

Method Details

defaultOutputs

public OutputEnabledMutable defaultOutputs()

Description copied from class: Task

If specified, default rules for determine which outputs are enabled or not.

Overrides:

defaultOutputs in class Task<NamedChannelsInput,NoSharedState>

Returns:

the default rules if they exist.

hasVeryQuickPerInputExecution

public boolean hasVeryQuickPerInputExecution()

Description copied from class: Task

Is the execution-time of the task per-input expected to be very quick to execute?

Specified by:

hasVeryQuickPerInputExecution in class Task<NamedChannelsInput,NoSharedState>

Returns:

true iff the execution is expected to be very quick, false otherwise.

beforeAnyJobIsExecuted

public NoSharedState beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<NamedChannelsInput> inputs,
 ParametersExperiment parameters)
                                     throws ExperimentExecutionException

Description copied from class: Task

Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

beforeAnyJobIsExecuted in class Task<NamedChannelsInput,NoSharedState>

Parameters:

outputter - the output-manager for the experiment (not for an individual job)

concurrencyPlan - available numbers of processors that can call Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)

inputs - a list of inputs, each will result in at least one call to Task.executeJob(ParametersUnbound).

parameters - the experiment-parameters.

Returns:

the shared-state that is passed to each call to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>) and to Task.afterAllJobsAreExecuted(S, org.anchoranalysis.io.output.outputter.InputOutputContext).

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

createSharedStateJob

protected OutputSequenceIndexed<Stack,String> createSharedStateJob(InputOutputContext context)
                                                            throws JobExecutionException

Sets a new output-sequence for the series.

It's important to do this here rather than in beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List, ParametersExperiment) as context is now bound with the directory/prefix related to the input.

Specified by:

createSharedStateJob in class RasterTask<NoSharedState,OutputSequenceIndexed<Stack,String>>

Parameters:

context - the input-output context associated with a particular job

Returns:

a newly created shared-state

Throws:

JobExecutionException - if an error occurs during job execution

startSeries

public void startSeries(NoSharedState sharedStateTask,
 OutputSequenceIndexed<Stack,String> sharedStateJob,
 InputOutputContext context)
                 throws JobExecutionException

Description copied from class: RasterTask

Starts processing of a series.

This corresponds to the start of an input job, before any stacks in the series are processed.

This should be called always once before all calls to RasterTask.doStack(org.anchoranalysis.experiment.task.InputBound<org.anchoranalysis.image.io.channel.input.NamedChannelsInput, S>, U, int, int, org.anchoranalysis.io.output.outputter.InputOutputContext).

Specified by:

startSeries in class RasterTask<NoSharedState,OutputSequenceIndexed<Stack,String>>

Parameters:

sharedStateTask - shared-state across all jobs in task

sharedStateJob - shared-state across all stacks in a job (i.e. in all series)

context - input-output context

Throws:

JobExecutionException - if an error occurs during job execution

doStack

public void doStack(InputBound<NamedChannelsInput,NoSharedState> input,
 OutputSequenceIndexed<Stack,String> sharedStateJob,
 int seriesIndex,
 int numberSeries,
 InputOutputContext context)
             throws JobExecutionException

Description copied from class: RasterTask

Processes one stack from a series.

This can be called many times in a job, once for each stack in the series.

It is assumed each job may have only one series.

Specified by:

doStack in class RasterTask<NoSharedState,OutputSequenceIndexed<Stack,String>>

Parameters:

input - the input-object corresponding to this stack (a set of named-channels)

sharedStateJob - shared-state across all stacks in a job (i.e. in all series)

seriesIndex - the index of the input that is being currently processed from the series

numberSeries - the total number of images in the series (constant for a given task)

context - IO context

Throws:

JobExecutionException - if an error occurs during job execution

endSeries

public void endSeries(NoSharedState sharedStateTask,
 OutputSequenceIndexed<Stack,String> sharedStateJob,
 InputOutputContext context)
               throws JobExecutionException

Description copied from class: RasterTask

Ends processing of a series.

This corresponds to the end of an input job, after any stacks in the series are processed.

This should be called always once after all calls to RasterTask.doStack(org.anchoranalysis.experiment.task.InputBound<org.anchoranalysis.image.io.channel.input.NamedChannelsInput, S>, U, int, int, org.anchoranalysis.io.output.outputter.InputOutputContext).

Specified by:

endSeries in class RasterTask<NoSharedState,OutputSequenceIndexed<Stack,String>>

Parameters:

sharedStateTask - shared-state across all jobs in task

sharedStateJob - shared-state across all stacks in a job (i.e. in all series)

context - input-output context

Throws:

JobExecutionException - if an error occurs during job execution

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(NoSharedState sharedState,
 InputOutputContext context)
                             throws ExperimentExecutionException

Description copied from class: Task

Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

afterAllJobsAreExecuted in class Task<NamedChannelsInput,NoSharedState>

Parameters:

sharedState - the shared-state

context - IO-context for experiment (not for an individual job)

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

getChannelConversionStyle

public ChannelConvertStyle getChannelConversionStyle()

To convert as RGB or independently or in another way.

setChannelConversionStyle

public void setChannelConversionStyle(ChannelConvertStyle channelConversionStyle)

To convert as RGB or independently or in another way.

isSuppressSeries

public boolean isSuppressSeries()

If true, the series index is not included in the outputted file-names.

It is always suppressed if only a single series exists.

setSuppressSeries

public void setSuppressSeries(boolean suppressSeries)

If true, the series index is not included in the outputted file-names.

It is always suppressed if only a single series exists.

getChannelConverter

public ConvertChannelTo<?> getChannelConverter()

Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)

setChannelConverter

public void setChannelConverter(ConvertChannelTo<?> channelConverter)

Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)