public class ExportObjectsAsCroppedImages extends ExportObjectsBase<MultiInput,NoSharedState>
The context is defined by a bounding-box is placed around an object-mask, and optionally padded.
Constructor and Description |
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ExportObjectsAsCroppedImages() |
Modifier and Type | Method and Description |
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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<MultiInput> inputs,
ParametersExperiment parameters)
Called once before all calls to
Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>) . |
OutputEnabledMutable |
defaultOutputs()
If specified, default rules for determine which outputs are enabled or not.
|
void |
doJobOnInput(InputBound<MultiInput,NoSharedState> input)
Performs the task on a particular input.
|
DefineOutputter |
getDefine() |
StackDisplayer |
getDisplayer()
How to convert an image to be displayed to the user.
|
List<NamedBean<StackProvider>> |
getListStackProvider()
The channels we extract the object-masks from - all assumed to be of same dimension
|
List<NamedBean<StackProvider>> |
getListStackProviderMIP()
The channels we extract the object-masks from - all assumed to be of same dimension
|
int |
getOutlineWidth() |
StringSet |
getOutputRGBOutline() |
StringSet |
getOutputRGBOutlineFlattened() |
boolean |
hasVeryQuickPerInputExecution()
Is the execution-time of the task per-input expected to be very quick to execute?
|
InputTypesExpected |
inputTypesExpected()
Highest class(es) that will function as a valid input.
|
boolean |
isExtendInZ()
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all
slices)
|
boolean |
isKeepEntireImage()
If true, rather than writing out a bounding-box around the object-mask, the entire image is
written
|
void |
setDefine(DefineOutputter define) |
void |
setDisplayer(StackDisplayer displayer)
How to convert an image to be displayed to the user.
|
void |
setExtendInZ(boolean extendInZ)
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all
slices)
|
void |
setKeepEntireImage(boolean keepEntireImage)
If true, rather than writing out a bounding-box around the object-mask, the entire image is
written
|
void |
setListStackProvider(List<NamedBean<StackProvider>> listStackProvider)
The channels we extract the object-masks from - all assumed to be of same dimension
|
void |
setListStackProviderMIP(List<NamedBean<StackProvider>> listStackProviderMIP)
The channels we extract the object-masks from - all assumed to be of same dimension
|
void |
setOutlineWidth(int outlineWidth) |
void |
setOutputRGBOutline(StringSet outputRGBOutline) |
void |
setOutputRGBOutlineFlattened(StringSet outputRGBOutlineFlattened) |
getObjects, getPadding, inputs, setObjects, setPadding
executeJob, isInputCompatibleWith
checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString
public void doJobOnInput(InputBound<MultiInput,NoSharedState> input) throws JobExecutionException
Task
doJobOnInput
in class Task<MultiInput,NoSharedState>
input
- the input for the job.JobExecutionException
- if an error occurs executing a particular job, that is not
otherwise suppressed.public InputTypesExpected inputTypesExpected()
Task
This is usually the class of T (or sometimes the absolute base class InputFromManager).
inputTypesExpected
in class Task<MultiInput,NoSharedState>
public boolean hasVeryQuickPerInputExecution()
Task
hasVeryQuickPerInputExecution
in class Task<MultiInput,NoSharedState>
public NoSharedState beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<MultiInput> inputs, ParametersExperiment parameters) throws ExperimentExecutionException
Task
Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)
.beforeAnyJobIsExecuted
in class Task<MultiInput,NoSharedState>
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.Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)
and to Task.afterAllJobsAreExecuted(S, org.anchoranalysis.io.output.outputter.InputOutputContext)
.ExperimentExecutionException
- if a fatal error occurs executing this step of the
experiment.public void afterAllJobsAreExecuted(NoSharedState sharedState, InputOutputContext context) throws ExperimentExecutionException
Task
Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)
.afterAllJobsAreExecuted
in class Task<MultiInput,NoSharedState>
sharedState
- the shared-statecontext
- IO-context for experiment (not for an individual job)ExperimentExecutionException
- if a fatal error occurs executing this step of the
experiment.public OutputEnabledMutable defaultOutputs()
Task
defaultOutputs
in class Task<MultiInput,NoSharedState>
public DefineOutputter getDefine()
public void setDefine(DefineOutputter define)
public List<NamedBean<StackProvider>> getListStackProvider()
public void setListStackProvider(List<NamedBean<StackProvider>> listStackProvider)
public List<NamedBean<StackProvider>> getListStackProviderMIP()
public void setListStackProviderMIP(List<NamedBean<StackProvider>> listStackProviderMIP)
public StringSet getOutputRGBOutline()
public void setOutputRGBOutline(StringSet outputRGBOutline)
public StringSet getOutputRGBOutlineFlattened()
public void setOutputRGBOutlineFlattened(StringSet outputRGBOutlineFlattened)
public int getOutlineWidth()
public void setOutlineWidth(int outlineWidth)
public boolean isExtendInZ()
public void setExtendInZ(boolean extendInZ)
public boolean isKeepEntireImage()
public void setKeepEntireImage(boolean keepEntireImage)
public StackDisplayer getDisplayer()
public void setDisplayer(StackDisplayer displayer)
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.