org.hkijena.jipipe.extensions.omero.algorithms

Class DownloadOMEROImageAlgorithm

java.lang.Object

org.hkijena.jipipe.api.nodes.JIPipeGraphNode

org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

org.hkijena.jipipe.api.nodes.JIPipeParameterSlotAlgorithm

org.hkijena.jipipe.api.nodes.JIPipeSimpleIteratingAlgorithm

org.hkijena.jipipe.extensions.omero.algorithms.DownloadOMEROImageAlgorithm

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class DownloadOMEROImageAlgorithm
extends JIPipeSimpleIteratingAlgorithm

Nested Class Summary

Nested classes/interfaces inherited from class org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

JIPipeAlgorithm.StateSerializer

Nested classes/interfaces inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

JIPipeGraphNode.BaseDirectoryChangedEvent, JIPipeGraphNode.Serializer

Nested classes/interfaces inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

JIPipeParameterCollection.ParameterChangedEvent, JIPipeParameterCollection.ParameterStructureChangedEvent, JIPipeParameterCollection.ParameterUIChangedEvent

Field Summary

Fields inherited from class org.hkijena.jipipe.api.nodes.JIPipeParameterSlotAlgorithm

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
DownloadOMEROImageAlgorithm(DownloadOMEROImageAlgorithm other)
DownloadOMEROImageAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
OMEColorMode	getColorMode()
OMEROCredentials	getCredentials()
RectangleList	getCropRegions()
ome.xml.model.enums.DimensionOrder	getStackOrder()
OptionalStringParameter	getTagAnnotation()
OptionalAnnotationNameParameter	getTitleAnnotation()
boolean	isAddKeyValuePairsAsAnnotations()
boolean	isAutoScale()
boolean	isConcatenate()
boolean	isCrop()
boolean	isExtractRois()
boolean	isSplitChannels()
boolean	isSplitFocalPlanes()
boolean	isSplitTimePoints()
boolean	isStitchTiles()
boolean	isSwapDimensions()
void	reportValidity(JIPipeIssueReport report) Generates a validity report
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	runParameterSet(JIPipeProgressInfo progressInfo, List<JIPipeTextAnnotation> parameterAnnotations) Runs a parameter set iteration
void	setAddKeyValuePairsAsAnnotations(boolean addKeyValuePairsAsAnnotations)
void	setAutoScale(boolean autoScale)
void	setColorMode(OMEColorMode colorMode)
void	setConcatenate(boolean concatenate)
void	setCrop(boolean crop)
void	setCropRegions(RectangleList cropRegions)
void	setExtractRois(boolean extractRois)
void	setSplitChannels(boolean splitChannels)
void	setSplitFocalPlanes(boolean splitFocalPlanes)
void	setSplitTimePoints(boolean splitTimePoints)
void	setStackOrder(ome.xml.model.enums.DimensionOrder stackOrder)
void	setStitchTiles(boolean stitchTiles)
void	setSwapDimensions(boolean swapDimensions)
void	setTagAnnotation(OptionalStringParameter tagAnnotation)
void	setTitleAnnotation(OptionalAnnotationNameParameter titleAnnotation)
boolean	supportsParallelization() Indicates to the algorithm base implementation if parallelization is supported.

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeSimpleIteratingAlgorithm

generateDataBatchesDryRun, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getParallelizationBatchSize, isParallelizationEnabled, isParameterUIVisible, isParameterUIVisible, runPassThrough, setParallelizationEnabled

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeParameterSlotAlgorithm

getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, run

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

canAutoPassThrough, canPassThrough, getStateId, getThreadPool, isEnabled, isPassThrough, isPostprocessor, isPreprocessor, loadExample, runPassThrough, setEnabled, setPassThrough, setThreadPool

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

canUserDelete, clearLocations, clearSlotData, copySlotConfiguration, duplicate, fromJson, fromJsonNode, getAliasIdInParentGraph, getBaseDirectory, getCategory, getCompartmentDisplayName, getCompartmentUUIDInGraphAsString, getCompartmentUUIDInParentGraph, getCustomDescription, getDependencies, getDisplayName, getEventBus, getFirstOutputSlot, getInfo, getInputSlot, getInputSlotMap, getInputSlotOrder, getInputSlots, getInputSlotsWithRole, getInternalStoragePath, getLastInputSlot, getLastOutputSlot, getLocations, getLocationWithin, getName, getNewScratch, getOpenInputSlots, getOutputSlot, getOutputSlotMap, getOutputSlots, getOutputSlotsWithRole, getParentGraph, getProjectCompartment, getProjectDirectory, getScratchBaseDirectory, getSlotConfiguration, getStoragePath, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isVisibleIn, onDeserialized, onParameterChanged, onParameterStructureChanged, onParameterUIChanged, onSlotConfigurationChanged, onSlotConnected, onSlotDisconnected, registerSubParameter, renderInputSlots, renderOutputSlots, setAllSlotsVirtual, setBaseDirectory, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setLocations, setLocationWithin, setLocationWithin, setParentGraph, setProjectDirectory, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, toggleSlot, toJson, triggerSlotsChangedEvent, updateGraphNodeSlots, updateSlotInheritance

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.hkijena.jipipe.api.JIPipeValidatable

generateValidityReport

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

addParameterChangeListener, addParameterChangeListener, getContextActions, getParameter, getParameterAccess, setParameter, triggerParameterChange, triggerParameterStructureChange, triggerParameterUIChange

Constructor Detail

DownloadOMEROImageAlgorithm

public DownloadOMEROImageAlgorithm(JIPipeNodeInfo info)

DownloadOMEROImageAlgorithm

public DownloadOMEROImageAlgorithm(DownloadOMEROImageAlgorithm other)

Method Detail

runParameterSet

public void runParameterSet(JIPipeProgressInfo progressInfo,
                            List<JIPipeTextAnnotation> parameterAnnotations)

Description copied from class: JIPipeParameterSlotAlgorithm

Runs a parameter set iteration

Overrides:

runParameterSet in class JIPipeSimpleIteratingAlgorithm

Parameters:

progressInfo - progress info from the run

parameterAnnotations - parameter annotations

runIteration

protected void runIteration(JIPipeDataBatch dataBatch,
                            JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeSimpleIteratingAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeSimpleIteratingAlgorithm

Parameters:

dataBatch - The data interface

progressInfo - the progress info from the run

getCredentials

public OMEROCredentials getCredentials()

reportValidity

public void reportValidity(JIPipeIssueReport report)

Description copied from interface: JIPipeValidatable

Generates a validity report

Specified by:

reportValidity in interface JIPipeValidatable

Overrides:

reportValidity in class JIPipeSimpleIteratingAlgorithm

Parameters:

report - the report to be added to

isAutoScale

public boolean isAutoScale()

setAutoScale

public void setAutoScale(boolean autoScale)

getColorMode

public OMEColorMode getColorMode()

setColorMode

public void setColorMode(OMEColorMode colorMode)

getCropRegions

public RectangleList getCropRegions()

setCropRegions

public void setCropRegions(RectangleList cropRegions)

getStackOrder

public ome.xml.model.enums.DimensionOrder getStackOrder()

setStackOrder

public void setStackOrder(ome.xml.model.enums.DimensionOrder stackOrder)

isSplitChannels

public boolean isSplitChannels()

setSplitChannels

public void setSplitChannels(boolean splitChannels)

isSplitFocalPlanes

public boolean isSplitFocalPlanes()

setSplitFocalPlanes

public void setSplitFocalPlanes(boolean splitFocalPlanes)

isSplitTimePoints

public boolean isSplitTimePoints()

setSplitTimePoints

public void setSplitTimePoints(boolean splitTimePoints)

isSwapDimensions

public boolean isSwapDimensions()

setSwapDimensions

public void setSwapDimensions(boolean swapDimensions)

isConcatenate

public boolean isConcatenate()

setConcatenate

public void setConcatenate(boolean concatenate)

isCrop

public boolean isCrop()

setCrop

public void setCrop(boolean crop)

isStitchTiles

public boolean isStitchTiles()

setStitchTiles

public void setStitchTiles(boolean stitchTiles)

getTitleAnnotation

public OptionalAnnotationNameParameter getTitleAnnotation()

setTitleAnnotation

public void setTitleAnnotation(OptionalAnnotationNameParameter titleAnnotation)

isExtractRois

public boolean isExtractRois()

setExtractRois

public void setExtractRois(boolean extractRois)

getTagAnnotation

public OptionalStringParameter getTagAnnotation()

setTagAnnotation

public void setTagAnnotation(OptionalStringParameter tagAnnotation)

isAddKeyValuePairsAsAnnotations

public boolean isAddKeyValuePairsAsAnnotations()

setAddKeyValuePairsAsAnnotations

public void setAddKeyValuePairsAsAnnotations(boolean addKeyValuePairsAsAnnotations)

supportsParallelization

public boolean supportsParallelization()

Description copied from interface: JIPipeParallelizedAlgorithm

Indicates to the algorithm base implementation if parallelization is supported. Use this function to indicate to the algorithm to conditionally enable/disable parallelization.

Specified by:

supportsParallelization in interface JIPipeParallelizedAlgorithm

Overrides:

supportsParallelization in class JIPipeSimpleIteratingAlgorithm

Returns:

If the algorithm supports automated parallelization.