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

Class ScaleImageCommonSize

Object

AnchorBean<Task<StackSequenceInput,CommonSize>>

Task<StackSequenceInput,CommonSize>

ScaleImage<CommonSize>

ScaleImageCommonSize

public class ScaleImageCommonSize
extends ScaleImage<CommonSize>

Creates a scaled copy of images, ensuring all images have identical output size.

When given input images of either varying or identical size, it will produce outputs of identical (scaled) size.

Whenever the scaled image is smaller than the output size, it is aligned (e.g. centered) and unused pixels are assigned the background color of 0.

Author:

Owen Feehan

Field Summary

Fields inherited from class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage

binary, scaleCalculator

Constructor Summary

Constructors

Constructor	Description
ScaleImageCommonSize()

Method Summary

Modifier and Type	Method	Description
CommonSize	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<StackSequenceInput> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
Align	getAlign()	How a smaller image (after scaling) is aligned to the larger image (with the common size).
int	getBackgroundIntensity()	The background intensity to use in each channel when the scaled image does not cover the entire canvas.
ImageMetadataReader	getImageMetadataReader()	How to read the ImageMetadata from the file-system.
StackReader	getStackReader()	Fallback for imageMetadataReader to read image files without a direct metadata reader.
protected Stack	scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, CommonSize sharedState)	Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.
void	setAlign(Align align)	How a smaller image (after scaling) is aligned to the larger image (with the common size).
void	setBackgroundIntensity(int backgroundIntensity)	The background intensity to use in each channel when the scaled image does not cover the entire canvas.
void	setImageMetadataReader(ImageMetadataReader imageMetadataReader)	How to read the ImageMetadata from the file-system.
void	setStackReader(StackReader stackReader)	Fallback for imageMetadataReader to read image files without a direct metadata reader.

Methods inherited from class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage

afterAllJobsAreExecuted, defaultOutputs, doJobOnInput, getInterpolator, getScaleCalculator, hasVeryQuickPerInputExecution, inputTypesExpected, isBinary, setBinary, setInterpolator, setScaleCalculator

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

ScaleImageCommonSize

public ScaleImageCommonSize()

Method Details

beforeAnyJobIsExecuted

public CommonSize beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<StackSequenceInput> 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<StackSequenceInput,CommonSize>

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.

scaleStack

protected Stack scaleStack(Stack stack,
 Optional<ImageSizeSuggestion> suggestedSize,
 VoxelsResizer voxelsResizer,
 CommonSize sharedState)
                    throws OperationFailedException

Description copied from class: ScaleImage

Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.

Specified by:

scaleStack in class ScaleImage<CommonSize>

Parameters:

stack - the stack before scaling.

suggestedSize - the suggested-size that has been passed into the task.

voxelsResizer - how to resize the voxels in a channel.

sharedState - the shared-state of the task.

Returns:

the scaled version of the stack.

Throws:

OperationFailedException - if the scaling operation fails.

getImageMetadataReader

public ImageMetadataReader getImageMetadataReader()

How to read the ImageMetadata from the file-system.

setImageMetadataReader

public void setImageMetadataReader(ImageMetadataReader imageMetadataReader)

How to read the ImageMetadata from the file-system.

getStackReader

public StackReader getStackReader()

Fallback for imageMetadataReader to read image files without a direct metadata reader.

setStackReader

public void setStackReader(StackReader stackReader)

Fallback for imageMetadataReader to read image files without a direct metadata reader.

getAlign

public Align getAlign()

How a smaller image (after scaling) is aligned to the larger image (with the common size).

e.g. centered, left-aligned etc. in each dimension.

setAlign

public void setAlign(Align align)

How a smaller image (after scaling) is aligned to the larger image (with the common size).

e.g. centered, left-aligned etc. in each dimension.

getBackgroundIntensity

public int getBackgroundIntensity()

The background intensity to use in each channel when the scaled image does not cover the entire canvas.

0 would create black, 255 would create white.

setBackgroundIntensity

public void setBackgroundIntensity(int backgroundIntensity)

The background intensity to use in each channel when the scaled image does not cover the entire canvas.

0 would create black, 255 would create white.