Uses of Class
org.hkijena.jipipe.api.JIPipeDocumentation

Packages that use JIPipeDocumentation

Package	Description
org.hkijena.jipipe
org.hkijena.jipipe.api
org.hkijena.jipipe.api.annotation
org.hkijena.jipipe.api.compartments.algorithms
org.hkijena.jipipe.api.compartments.datatypes
org.hkijena.jipipe.api.compat
org.hkijena.jipipe.api.data
org.hkijena.jipipe.api.environments
org.hkijena.jipipe.api.grouping
org.hkijena.jipipe.api.grouping.parameters
org.hkijena.jipipe.api.looping
org.hkijena.jipipe.api.nodes
org.hkijena.jipipe.api.parameters
org.hkijena.jipipe.extensions.annotation.algorithms
org.hkijena.jipipe.extensions.annotation.datasources
org.hkijena.jipipe.extensions.batchassistant
org.hkijena.jipipe.extensions.cellpose
org.hkijena.jipipe.extensions.cellpose.algorithms
org.hkijena.jipipe.extensions.cellpose.algorithms.deprecated
org.hkijena.jipipe.extensions.cellpose.compat
org.hkijena.jipipe.extensions.cellpose.datatypes
org.hkijena.jipipe.extensions.cellpose.installers
org.hkijena.jipipe.extensions.cellpose.parameters
org.hkijena.jipipe.extensions.cellpose.parameters.deprecated
org.hkijena.jipipe.extensions.clij2
org.hkijena.jipipe.extensions.clij2.algorithms
org.hkijena.jipipe.extensions.clij2.compat
org.hkijena.jipipe.extensions.clij2.datatypes
org.hkijena.jipipe.extensions.core.nodes
org.hkijena.jipipe.extensions.expressions.constants
org.hkijena.jipipe.extensions.expressions.functions
org.hkijena.jipipe.extensions.expressions.functions.collections
org.hkijena.jipipe.extensions.expressions.functions.color
org.hkijena.jipipe.extensions.expressions.functions.control
org.hkijena.jipipe.extensions.expressions.functions.convert
org.hkijena.jipipe.extensions.expressions.functions.datetime
org.hkijena.jipipe.extensions.expressions.functions.filesystem
org.hkijena.jipipe.extensions.expressions.functions.functions
org.hkijena.jipipe.extensions.expressions.functions.math
org.hkijena.jipipe.extensions.expressions.functions.quantities
org.hkijena.jipipe.extensions.expressions.functions.statistics
org.hkijena.jipipe.extensions.expressions.functions.string
org.hkijena.jipipe.extensions.expressions.functions.util
org.hkijena.jipipe.extensions.expressions.functions.variables
org.hkijena.jipipe.extensions.expressions.operators
org.hkijena.jipipe.extensions.filesystem
org.hkijena.jipipe.extensions.filesystem.algorithms
org.hkijena.jipipe.extensions.filesystem.compat
org.hkijena.jipipe.extensions.filesystem.datasources
org.hkijena.jipipe.extensions.filesystem.dataypes
org.hkijena.jipipe.extensions.forms.algorithms
org.hkijena.jipipe.extensions.forms.datatypes
org.hkijena.jipipe.extensions.forms.utils
org.hkijena.jipipe.extensions.ijmultitemplatematching
org.hkijena.jipipe.extensions.ijtrackmate.datatypes
org.hkijena.jipipe.extensions.ijtrackmate.nodes.converters
org.hkijena.jipipe.extensions.ijtrackmate.nodes.detectors
org.hkijena.jipipe.extensions.ijtrackmate.nodes.spots
org.hkijena.jipipe.extensions.ijtrackmate.nodes.tracks
org.hkijena.jipipe.extensions.ijtrackmate.parameters
org.hkijena.jipipe.extensions.ijtrackmate.settings
org.hkijena.jipipe.extensions.ijtrackmate.utils
org.hkijena.jipipe.extensions.ijweka.datatypes
org.hkijena.jipipe.extensions.ijweka.nodes
org.hkijena.jipipe.extensions.ijweka.parameters
org.hkijena.jipipe.extensions.ijweka.parameters.collections
org.hkijena.jipipe.extensions.imagej2
org.hkijena.jipipe.extensions.imagej2.algorithms
org.hkijena.jipipe.extensions.imagej2.compat
org.hkijena.jipipe.extensions.imagej2.datatypes
org.hkijena.jipipe.extensions.imagej2.datatypes.outofbounds
org.hkijena.jipipe.extensions.imagej2.datatypes.outofbounds.constant
org.hkijena.jipipe.extensions.imagej2.datatypes.shapes
org.hkijena.jipipe.extensions.imagejalgorithms.ij1
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.analyze
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.background
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.binary
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.blur
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.calibration
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.colocalization
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.color
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.contrast
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.convert
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.convolve
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.datasources
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.dimensions
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.edge
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.features
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.fft
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.forms
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.generate
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.io
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels.filter
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.lut
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math.distancemap
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math.local
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.misc
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.morphology
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.noise
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.opticalflow
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.overlay
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.annotations
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.assemble
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.convert
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.draw
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.filter
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.generate
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.measure
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.merge
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.modify
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.properties
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.sort
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.split
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.segment
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.sharpen
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.statistics
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.color
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.iterative
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.local
org.hkijena.jipipe.extensions.imagejalgorithms.ij1.transform
org.hkijena.jipipe.extensions.imagejalgorithms.utils
org.hkijena.jipipe.extensions.imagejdatatypes
org.hkijena.jipipe.extensions.imagejdatatypes.algorithms
org.hkijena.jipipe.extensions.imagejdatatypes.algorithms.color
org.hkijena.jipipe.extensions.imagejdatatypes.algorithms.datasources
org.hkijena.jipipe.extensions.imagejdatatypes.compat
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.color
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2.color
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2.greyscale
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3.color
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3.greyscale
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4.color
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4.greyscale
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5.color
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5.greyscale
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.fft
org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.greyscale
org.hkijena.jipipe.extensions.imagejdatatypes.parameters
org.hkijena.jipipe.extensions.imagejdatatypes.settings
org.hkijena.jipipe.extensions.imagejdatatypes.util
org.hkijena.jipipe.extensions.imageviewer.plugins.maskdrawer
org.hkijena.jipipe.extensions.imageviewer.plugins.roimanager
org.hkijena.jipipe.extensions.multiparameters.datatypes
org.hkijena.jipipe.extensions.multiparameters.nodes
org.hkijena.jipipe.extensions.omero
org.hkijena.jipipe.extensions.omero.algorithms
org.hkijena.jipipe.extensions.omero.datasources
org.hkijena.jipipe.extensions.omero.datatypes
org.hkijena.jipipe.extensions.omnipose
org.hkijena.jipipe.extensions.omnipose.algorithms
org.hkijena.jipipe.extensions.omnipose.installers
org.hkijena.jipipe.extensions.omnipose.parameters
org.hkijena.jipipe.extensions.parameters.api.enums
org.hkijena.jipipe.extensions.parameters.library.primitives
org.hkijena.jipipe.extensions.parameters.library.references
org.hkijena.jipipe.extensions.parameters.library.roi
org.hkijena.jipipe.extensions.pipelinerender
org.hkijena.jipipe.extensions.plots.datatypes
org.hkijena.jipipe.extensions.plots.nodes
org.hkijena.jipipe.extensions.processes
org.hkijena.jipipe.extensions.python
org.hkijena.jipipe.extensions.python.algorithms
org.hkijena.jipipe.extensions.python.installers
org.hkijena.jipipe.extensions.r
org.hkijena.jipipe.extensions.r.algorithms
org.hkijena.jipipe.extensions.r.installers
org.hkijena.jipipe.extensions.settings
org.hkijena.jipipe.extensions.strings
org.hkijena.jipipe.extensions.strings.datasources
org.hkijena.jipipe.extensions.tables.compat
org.hkijena.jipipe.extensions.tables.datatypes
org.hkijena.jipipe.extensions.tables.nodes
org.hkijena.jipipe.extensions.tables.nodes.annotations
org.hkijena.jipipe.extensions.tables.nodes.columns
org.hkijena.jipipe.extensions.tables.nodes.filter
org.hkijena.jipipe.extensions.tables.nodes.merge
org.hkijena.jipipe.extensions.tables.nodes.rows
org.hkijena.jipipe.extensions.tables.nodes.split
org.hkijena.jipipe.extensions.tables.nodes.transform
org.hkijena.jipipe.extensions.tables.parameters.enums
org.hkijena.jipipe.extensions.utils.algorithms
org.hkijena.jipipe.extensions.utils.algorithms.datatable
org.hkijena.jipipe.extensions.utils.algorithms.distribute
org.hkijena.jipipe.extensions.utils.algorithms.meta
org.hkijena.jipipe.extensions.utils.algorithms.processes
org.hkijena.jipipe.extensions.utils.datatypes
org.hkijena.jipipe.ui.cache.exporters
org.hkijena.jipipe.ui.components
org.hkijena.jipipe.ui.grapheditor.general.properties
org.hkijena.jipipe.ui.parameters
org.hkijena.jipipe.ui.plotbuilder
org.hkijena.jipipe.ui.quickrun
org.hkijena.jipipe.utils

Uses of JIPipeDocumentation in org.hkijena.jipipe

Methods in org.hkijena.jipipe with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	JIPipeMutableDependency.getDependencyId()
String	JIPipeJsonExtension.getDependencyId()
String	JIPipeMutableDependency.getDependencyVersion()
String	JIPipeJsonExtension.getDependencyVersion()
String	JIPipeImageJUpdateSiteDependency.getDescription()
String	JIPipeImageJUpdateSiteDependency.getMaintainer()
JIPipeMetadata	JIPipeMutableDependency.getMetadata()
JIPipeMetadata	JIPipeJsonExtension.getMetadata()
String	JIPipeImageJUpdateSiteDependency.getName()
JIPipeImageJUpdateSiteDependency.List	JIPipeJsonExtension.getUpdateSiteDependenciesParameter()
String	JIPipeImageJUpdateSiteDependency.getUrl()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api

Methods in org.hkijena.jipipe.api with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeAuthorMetadata.List	JIPipeMetadata.getAcknowledgements() Gets the list of acknowledged authors
StringList	JIPipeAuthorMetadata.getAffiliations()
JIPipeAuthorMetadata.List	JIPipeMetadata.getAuthors()
Color	JIPipeNodeTemplate.getBorderColor()
PluginCategoriesEnumParameter.List	JIPipeMetadata.getCategories()
String	JIPipeMetadata.getCitation()
String	JIPipeAuthorMetadata.getContact()
HTMLText	JIPipeAuthorMetadata.getCustomText()
String	JIPipeNodeTemplate.getData()
StringList	JIPipeMetadata.getDependencyCitations()
HTMLText	JIPipeNodeTemplate.getDescription()
HTMLText	JIPipeMetadata.getDescription()
Color	JIPipeNodeTemplate.getFillColor()
String	JIPipeAuthorMetadata.getFirstName()
IconRef	JIPipeNodeTemplate.getIcon()
String	JIPipeAuthorMetadata.getLastName()
String	JIPipeMetadata.getLicense()
StringList	JIPipeNodeTemplate.getMenuPath()
String	JIPipeNodeTemplate.getName()
String	JIPipeMetadata.getName()
JIPipeNodeTemplate.List	JIPipeProjectMetadata.getNodeTemplates()
int	JIPipeRunSettings.getNumThreads()
Path	JIPipeRunSettings.getOutputPath()
JIPipeProjectPermissions	JIPipeProjectMetadata.getPermissions()
String	JIPipeNodeTemplate.getSource()
HTMLText	JIPipeMetadata.getSummary()
String	JIPipeProjectMetadata.getTemplateDescription()
ImageParameter	JIPipeMetadata.getThumbnail()
String	JIPipeAuthorMetadata.getTitle()
JIPipeImageJUpdateSiteDependency.List	JIPipeProjectMetadata.getUpdateSiteDependencies()
String	JIPipeMetadata.getWebsite()
String	JIPipeAuthorMetadata.getWebsite()
boolean	JIPipeAuthorMetadata.isCorrespondingAuthor()
boolean	JIPipeAuthorMetadata.isFirstAuthor()
boolean	JIPipeRunSettings.isLoadFromCache()
boolean	JIPipeProjectPermissions.isPreventAddingDeletingNodes()
boolean	JIPipeProjectPermissions.isPreventModifyingSlots()
boolean	JIPipeProjectMetadata.isRestoreTabs()
boolean	JIPipeRunSettings.isStoreToCache()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.annotation

Methods in org.hkijena.jipipe.api.annotation with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DefaultExpressionParameter	JIPipeDataByMetadataExporter.getFileNameGenerator()
boolean	JIPipeDataByMetadataExporter.isForceName()
boolean	JIPipeDataByMetadataExporter.isMakeFilesystemCompatible()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.compartments.algorithms

Classes in org.hkijena.jipipe.api.compartments.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	IOInterfaceAlgorithm Algorithm that passes the input to the output
class	JIPipeCompartmentOutput A graph compartment output Transfers data 1:1 from input to output
class	JIPipeProjectCompartment A project compartment.

Methods in org.hkijena.jipipe.api.compartments.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
GraphNodeParameterReferenceGroupCollection	JIPipeProjectCompartment.getExportedParameters()
boolean	JIPipeProjectCompartment.isShowLimitedParameters()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.compartments.datatypes

Classes in org.hkijena.jipipe.api.compartments.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	JIPipeCompartmentOutputData Represents an JIPipeCompartmentOutput in the compartment graph.

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.compat

Classes in org.hkijena.jipipe.api.compat with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DataTableImageJDataExporter The fallback/default data adapter that can handle any data type.
class	DataTableImageJDataImporter The fallback/default data adapter that can handle any data type.
class	EmptyImageJDataExporter An exporter that does nothing
class	EmptyImageJDataImporter An importer that does nothing

Methods in org.hkijena.jipipe.api.compat with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	ImageJDataExportOperation.getExporterId()
String	ImageJDataImportOperation.getImporterId()
String	ImageJImportParameters.getName()
String	ImageJExportParameters.getName()
boolean	ImageJExportParameters.isActivate()
boolean	ImageJExportParameters.isAppend()
boolean	ImageJImportParameters.isDuplicate()
boolean	ImageJExportParameters.isDuplicate()
boolean	ImageJExportParameters.isNoWindows()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.data

Classes in org.hkijena.jipipe.api.data with annotations of type JIPipeDocumentation

Modifier and Type	Interface and Description
interface	JIPipeData Base class for any JIPipe data wrapper class There must be a static function importData(JIPipeReadDataStorage, JIPipeProgressInfo) that imports the data from a row storage folder.
class	JIPipeDataTable
class	JIPipeEmptyData

Methods in org.hkijena.jipipe.api.data with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	JIPipeDataSlotInfo.getCustomName()
String	JIPipeDataSlotInfo.getDescription()
boolean	JIPipeDataSlotInfo.isOptional()
boolean	JIPipeDataSlotInfo.isSaveOutputs()
boolean	JIPipeDataSlotInfo.isVirtual()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.environments

Methods in org.hkijena.jipipe.api.environments with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	ExternalEnvironment.getName()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.grouping

Classes in org.hkijena.jipipe.api.grouping with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	GraphWrapperAlgorithmInput
class	GraphWrapperAlgorithmOutput
class	NodeGroup A sub-graph algorithm that can be defined by a user

Methods in org.hkijena.jipipe.api.grouping with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeMergingAlgorithmDataBatchGenerationSettings	JsonAlgorithm.getBatchGenerationSettings()
JIPipeMergingAlgorithmDataBatchGenerationSettings	NodeGroup.getBatchGenerationSettings()
DynamicCategoryEnumParameter	JsonNodeInfo.getCategoryParameter()
NodeGroupContents	NodeGroup.getContents()
IconRef	JsonNodeInfo.getCustomIcon()
HTMLText	JsonNodeInfo.getDescription()
GraphNodeParameterReferenceGroupCollection	JsonNodeInfo.getExportedParameters()
GraphNodeParameterReferenceGroupCollection	NodeGroup.getExportedParameters()
String	JsonNodeInfo.getId()
GraphWrapperAlgorithm.IterationMode	JsonAlgorithm.getIterationMode()
GraphWrapperAlgorithm.IterationMode	NodeGroup.getIterationMode()
StringList	JsonNodeInfo.getMenuPathList()
String	JsonNodeInfo.getName()
boolean	JsonNodeInfo.isHidden()
boolean	NodeGroup.isShowLimitedParameters()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.grouping.parameters

Methods in org.hkijena.jipipe.api.grouping.parameters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
HTMLText	GraphNodeParameterReference.getCustomDescription()
String	GraphNodeParameterReference.getCustomName()
HTMLText	GraphNodeParameterReferenceGroup.getDescription()
String	GraphNodeParameterReferenceGroup.getName()
String	GraphNodeParameterReference.getPath()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.looping

Classes in org.hkijena.jipipe.api.looping with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	LoopEndNode
class	LoopStartNode

Methods in org.hkijena.jipipe.api.looping with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeMergingAlgorithmDataBatchGenerationSettings	LoopStartNode.getBatchGenerationSettings()
GraphWrapperAlgorithm.IterationMode	LoopStartNode.getIterationMode()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.nodes

Methods in org.hkijena.jipipe.api.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeAdaptiveParameterSettings	JIPipeSingleIterationAlgorithm.getAdaptiveParameterSettings()
JIPipeAdaptiveParameterSettings	JIPipeMergingAlgorithm.getAdaptiveParameterSettings()
JIPipeAdaptiveParameterSettings	JIPipeIteratingAlgorithm.getAdaptiveParameterSettings()
JIPipeAdaptiveParameterSettings	JIPipeSimpleIteratingAlgorithm.getAdaptiveParameterSettings()
JIPipeTextAnnotationMatchingMethod	JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings.getAnnotationMatchingMethod()
JIPipeTextAnnotationMatchingMethod	JIPipeIteratingAlgorithmDataBatchGenerationSettings.getAnnotationMatchingMethod()
JIPipeTextAnnotationMatchingMethod	JIPipeMergingAlgorithmDataBatchGenerationSettings.getAnnotationMatchingMethod()
JIPipeTextAnnotationMergeMode	JIPipeSingleIterationAlgorithmDataBatchGenerationSettings.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	JIPipeIteratingAlgorithmDataBatchGenerationSettings.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	JIPipeMergingAlgorithmDataBatchGenerationSettings.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	JIPipeMissingDataGeneratorDataBatchGenerationSettings.getAnnotationMergeStrategy()
JIPipeColumMatching	JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings.getColumnMatching()
JIPipeColumMatching	JIPipeIteratingAlgorithmDataBatchGenerationSettings.getColumnMatching()
JIPipeColumMatching	JIPipeMergingAlgorithmDataBatchGenerationSettings.getColumnMatching()
DefaultExpressionParameter	JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings.getCustomAnnotationMatching()
DefaultExpressionParameter	JIPipeIteratingAlgorithmDataBatchGenerationSettings.getCustomAnnotationMatching()
DefaultExpressionParameter	JIPipeMergingAlgorithmDataBatchGenerationSettings.getCustomAnnotationMatching()
StringQueryExpression	JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings.getCustomColumns()
StringQueryExpression	JIPipeIteratingAlgorithmDataBatchGenerationSettings.getCustomColumns()
StringQueryExpression	JIPipeMergingAlgorithmDataBatchGenerationSettings.getCustomColumns()
StringQueryExpression	JIPipeMissingDataGeneratorDataBatchGenerationSettings.getCustomColumns()
HTMLText	JIPipeGraphNode.getCustomDescription() Returns the custom description that is set by the user
JIPipeDataAnnotationMergeMode	JIPipeSingleIterationAlgorithmDataBatchGenerationSettings.getDataAnnotationMergeStrategy()
JIPipeDataAnnotationMergeMode	JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings.getDataAnnotationMergeStrategy()
JIPipeDataAnnotationMergeMode	JIPipeIteratingAlgorithmDataBatchGenerationSettings.getDataAnnotationMergeStrategy()
JIPipeDataAnnotationMergeMode	JIPipeMergingAlgorithmDataBatchGenerationSettings.getDataAnnotationMergeStrategy()
JIPipeDataAnnotationMergeMode	JIPipeMissingDataGeneratorDataBatchGenerationSettings.getDataAnnotationMergeStrategy()
JIPipeSingleIterationAlgorithmDataBatchGenerationSettings	JIPipeSingleIterationAlgorithm.getDataBatchGenerationSettings()
JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings	JIPipeIteratingMissingDataGeneratorAlgorithm.getDataBatchGenerationSettings()
JIPipeMergingAlgorithmDataBatchGenerationSettings	JIPipeMergingAlgorithm.getDataBatchGenerationSettings()
JIPipeParameterlessSimpleIteratingAlgorithm.DataBatchGenerationSettings	JIPipeParameterlessSimpleIteratingAlgorithm.getDataBatchGenerationSettings()
JIPipeMissingDataGeneratorDataBatchGenerationSettings	JIPipeMissingDataGeneratorAlgorithm.getDataBatchGenerationSettings()
JIPipeIteratingAlgorithmDataBatchGenerationSettings	JIPipeIteratingAlgorithm.getDataBatchGenerationSettings()
JIPipeSimpleIteratingAlgorithmDataBatchGenerationSettings	JIPipeSimpleIteratingAlgorithm.getDataBatchGenerationSettings()
JIPipeColumMatching	JIPipeMissingDataGeneratorDataBatchGenerationSettings.getDataSetMatching()
OptionalIntegerRange	JIPipeSimpleIteratingAlgorithmDataBatchGenerationSettings.getLimit()
OptionalIntegerRange	JIPipeParameterlessSimpleIteratingAlgorithm.DataBatchGenerationSettings.getLimit()
OptionalIntegerRange	JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings.getLimit()
OptionalIntegerRange	JIPipeIteratingAlgorithmDataBatchGenerationSettings.getLimit()
OptionalIntegerRange	JIPipeMergingAlgorithmDataBatchGenerationSettings.getLimit()
OptionalIntegerRange	JIPipeMissingDataGeneratorDataBatchGenerationSettings.getLimit()
String	JIPipeGraphNode.getName() Returns the algorithm name
StringQueryExpressionAndStringPairParameter.List	JIPipeAdaptiveParameterSettings.getOverriddenParameters()
String	JIPipeAdaptiveParameterSettings.getParameterAnnotationsPrefix()
String	JIPipeParameterSlotAlgorithmSettings.getParameterAnnotationsPrefix()
JIPipeParameterSlotAlgorithmSettings	JIPipeParameterSlotAlgorithm.getParameterSlotAlgorithmSettings()
boolean	JIPipeMissingDataGeneratorDataBatchGenerationSettings.isAllowMerging()
boolean	JIPipeAdaptiveParameterSettings.isAttachOnlyNonDefaultParameterAnnotations()
boolean	JIPipeParameterSlotAlgorithmSettings.isAttachOnlyNonDefaultParameterAnnotations()
boolean	JIPipeAdaptiveParameterSettings.isAttachParameterAnnotations()
boolean	JIPipeParameterSlotAlgorithmSettings.isAttachParameterAnnotations()
boolean	JIPipeGraphNode.isBookmarked()
boolean	JIPipeAlgorithm.isEnabled()
boolean	JIPipeAdaptiveParameterSettings.isEnabled()
boolean	JIPipeIteratingMissingDataGeneratorDataBatchGenerationSettings.isForceFlowGraphSolver()
boolean	JIPipeIteratingAlgorithmDataBatchGenerationSettings.isForceFlowGraphSolver()
boolean	JIPipeMergingAlgorithmDataBatchGenerationSettings.isForceFlowGraphSolver()
boolean	JIPipeMissingDataGeneratorDataBatchGenerationSettings.isForceFlowGraphSolver()
boolean	JIPipeParameterSlotAlgorithmSettings.isHasParameterSlot()
boolean	JIPipeIteratingMissingDataGeneratorAlgorithm.isKeepOriginalAnnotations()
boolean	JIPipeMissingDataGeneratorAlgorithm.isKeepOriginalAnnotations()
boolean	JIPipeSingleIterationAlgorithm.isParallelizationEnabled()
boolean	JIPipeIteratingMissingDataGeneratorAlgorithm.isParallelizationEnabled()
boolean	JIPipeMergingAlgorithm.isParallelizationEnabled()
boolean	JIPipeParameterlessSimpleIteratingAlgorithm.isParallelizationEnabled()
boolean	JIPipeMissingDataGeneratorAlgorithm.isParallelizationEnabled()
boolean	JIPipeIteratingAlgorithm.isParallelizationEnabled()
boolean	JIPipeSimpleIteratingAlgorithm.isParallelizationEnabled()
boolean	JIPipeAdaptiveParameterSettings.isParameterAnnotationsUseInternalNames()
boolean	JIPipeParameterSlotAlgorithmSettings.isParameterAnnotationsUseInternalNames()
boolean	JIPipeAlgorithm.isPassThrough()
boolean	JIPipeIteratingAlgorithmDataBatchGenerationSettings.isSkipIncompleteDataSets()
boolean	JIPipeMergingAlgorithmDataBatchGenerationSettings.isSkipIncompleteDataSets()

Uses of JIPipeDocumentation in org.hkijena.jipipe.api.parameters

Methods in org.hkijena.jipipe.api.parameters that return JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeDocumentation	JIPipeDefaultParameterCollectionContextAction.getDocumentation()
JIPipeDocumentation	JIPipeReflectionParameterAccess.getDocumentation()
JIPipeDocumentation	JIPipeReflectionParameterCollectionContextAction.getDocumentation()
JIPipeDocumentation	JIPipeParameterCollectionContextAction.getDocumentation() Documentation of this action
JIPipeDocumentation	JIPipeParameterTree.getSourceDocumentation(JIPipeParameterCollection source) Gets source documentation

Methods in org.hkijena.jipipe.api.parameters with parameters of type JIPipeDocumentation

Modifier and Type	Method and Description
void	JIPipeReflectionParameterAccess.setDocumentation(JIPipeDocumentation documentation)

Constructors in org.hkijena.jipipe.api.parameters with parameters of type JIPipeDocumentation

Constructor and Description
JIPipeDefaultParameterCollectionContextAction(JIPipeDocumentation documentation, URL iconURL, Consumer<JIPipeWorkbench> function)
JIPipeReflectionParameterCollectionContextAction(Object target, Method function, URL iconURL, JIPipeDocumentation documentation)

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.annotation.algorithms

Classes in org.hkijena.jipipe.extensions.annotation.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AnnotateByExpression Algorithm that annotates all data with the same annotation
class	AnnotateWithAnnotationTable Algorithm that merges the annotations of all inputs and outputs the data with the shared annotations
class	AnnotateWithData
class	AnnotateWithDataString Generates annotations from filenames
class	AnnotateWithSourceSlot Generates annotations from filenames
class	ConvertToAnnotationTable Removes a specified annotation
class	DataAnnotationToStringAnnotation
class	ExtractAndReplaceAnnotation Generates annotations from filenames
class	ExtractDataAnnotation
class	FilterByAnnotation Algorithm that splits the input data by a specified annotation
class	GenerateRandomUniqueAnnotation Generates annotations from filenames
class	GenerateUniqueAnnotation Generates annotations from filenames
class	MergeAnnotations Algorithm that merges the annotations of all inputs and outputs the data with the shared annotations
class	MergeDataSlots Merges the input slot tables into one data slot
class	ModifyAnnotationScript Algorithm that annotates all data with the same annotation
class	OverwriteAnnotations
class	RemoveAnnotationAlgorithm Removes a specified annotation
class	RemoveArrayAnnotationsAlgorithm
class	RemoveDataAnnotations
class	RemoveNAAnnotationColumnsAlgorithm
class	RenameAnnotation Generates annotations from filenames
class	RenameDataAnnotation Generates annotations from filenames
class	SetSingleAnnotation Algorithm that annotates all data with the same annotation
class	SimplifyAnnotationsAlgorithm
class	SplitByAnnotation Algorithm that splits the input data by a specified annotation
class	SplitByAnnotationScript Algorithm that annotates all data with the same annotation

Methods in org.hkijena.jipipe.extensions.annotation.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalAnnotationNameParameter	ConvertToAnnotationTable.getAddDataToString()
OptionalStringParameter	ExtractDataAnnotation.getAnnotateWithCurrentData()
AnnotationQueryExpression	RemoveAnnotationAlgorithm.getAnnotationExpression()
AnnotationQueryExpression	SimplifyAnnotationsAlgorithm.getAnnotationFilter()
JIPipeDataAnnotationMergeMode	RenameDataAnnotation.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	GenerateRandomUniqueAnnotation.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	GenerateUniqueAnnotation.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	AnnotateWithData.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	AnnotateWithSourceSlot.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	DataAnnotationToStringAnnotation.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	AnnotateByExpression.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	RenameAnnotation.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	AnnotateWithDataString.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	ExtractAndReplaceAnnotation.getAnnotationMergeStrategy()
String	AnnotateWithData.getAnnotationName()
StringQueryExpression	SetSingleAnnotation.getAnnotationName()
StringQueryExpression	RemoveArrayAnnotationsAlgorithm.getAnnotationNameFilter()
StringQueryExpression	RemoveNAAnnotationColumnsAlgorithm.getAnnotationNameFilter()
StringQueryExpression	ExtractDataAnnotation.getAnnotationNameQuery()
SimplifyAnnotationsAlgorithm.AnnotationRemovalMode	SimplifyAnnotationsAlgorithm.getAnnotationRemovalMode()
NamedTextAnnotationGeneratorExpression.List	AnnotateByExpression.getAnnotations()
StringQueryExpression	SetSingleAnnotation.getAnnotationValue()
String	GenerateUniqueAnnotation.getBaseName()
PythonScript	SplitByAnnotationScript.getCode()
PythonScript	ModifyAnnotationScript.getCode()
DefaultExpressionParameter	SimplifyAnnotationsAlgorithm.getCombinationFunction()
CustomExpressionVariablesParameter	SplitByAnnotation.getCustomVariables()
CustomExpressionVariablesParameter	AnnotateByExpression.getCustomVariables()
CustomExpressionVariablesParameter	FilterByAnnotation.getCustomVariables()
CustomExpressionVariablesParameter	OverwriteAnnotations.getCustomVariables()
AnnotationFilterExpression	FilterByAnnotation.getFilter()
StringPatternExtractionFunction.List	ExtractAndReplaceAnnotation.getFunctions()
String	GenerateRandomUniqueAnnotation.getGeneratedAnnotation()
String	GenerateUniqueAnnotation.getGeneratedAnnotation()
String	AnnotateWithSourceSlot.getGeneratedAnnotation()
String	AnnotateWithDataString.getGeneratedAnnotation()
String	SimplifyAnnotationsAlgorithm.getGeneratedAnnotationName()
JIPipeTextAnnotationMergeMode	OverwriteAnnotations.getMergeMode()
StringQueryExpression	DataAnnotationToStringAnnotation.getNameFilter()
StringQueryExpression	RemoveDataAnnotations.getNameFilter()
DefaultExpressionParameter	OverwriteAnnotations.getRemoveExistingAnnotationsFilter()
StringQueryExpression	SimplifyAnnotationsAlgorithm.getRenameFunction()
StringQueryExpressionAndStringPairParameter.List	RenameDataAnnotation.getRenamingItems()
StringQueryExpressionAndStringPairParameter.List	RenameAnnotation.getRenamingItems()
JIPipeDynamicParameterCollection	SplitByAnnotationScript.getScriptParameters()
JIPipeDynamicParameterCollection	ModifyAnnotationScript.getScriptParameters()
DefaultExpressionParameter	OverwriteAnnotations.getSourceAnnotationFilter()
JIPipeIteratingAlgorithmDataBatchGenerationSettings	AnnotateWithAnnotationTable.getTableMergeSettings()
OutputSlotMapParameterCollection	SplitByAnnotation.getTargetSlots()
boolean	AnnotateWithDataString.isDetailedDataString()
boolean	AnnotateWithAnnotationTable.isDiscardExistingAnnotations()
boolean	ExtractDataAnnotation.isIgnoreMissingAnnotations()
boolean	ExtractDataAnnotation.isKeepCurrentAnnotation()
boolean	DataAnnotationToStringAnnotation.isKeepDataAnnotations()
boolean	ExtractDataAnnotation.isKeepOtherDataAnnotations()
boolean	AnnotateWithData.isMergeInputAnnotations()
boolean	AnnotateWithData.isMergeLabelAnnotations()
boolean	RemoveArrayAnnotationsAlgorithm.isRemoveColumn()
boolean	ConvertToAnnotationTable.isRemoveOutputAnnotations()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.annotation.datasources

Classes in org.hkijena.jipipe.extensions.annotation.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AnnotationTableFromFile Imports AnnotationTableData from a file

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.batchassistant

Classes in org.hkijena.jipipe.extensions.batchassistant with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DataBatchStatusData

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.cellpose

Methods in org.hkijena.jipipe.extensions.cellpose with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
StringList	CellposeSettings.getEasyInstallerRepositories()
OptionalPythonEnvironment	CellposeSettings.getOverridePythonEnvironment()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.cellpose.algorithms

Classes in org.hkijena.jipipe.extensions.cellpose.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CellposeAlgorithm Improved version of CellposeAlgorithm_Old that utilizes the Cellpose CLI
class	CellposeTrainingAlgorithm
class	ImportCellposeModelAlgorithm
class	ImportCellposeSizeModelAlgorithm

Methods in org.hkijena.jipipe.extensions.cellpose.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
CellposeChannelSettings	CellposeTrainingAlgorithm.getChannelSettings()
CellposeChannelSettings	CellposeAlgorithm.getChannelSettings()
OptionalDoubleParameter	CellposeTrainingAlgorithm.getDiameter()
OptionalDoubleParameter	CellposeAlgorithm.getDiameter()
OptionalAnnotationNameParameter	CellposeAlgorithm.getDiameterAnnotation()
CellposeSegmentationTweaksSettings	CellposeAlgorithm.getEnhancementParameters()
CellposeGPUSettings	CellposeTrainingAlgorithm.getGpuSettings()
CellposeGPUSettings	CellposeAlgorithm.getGpuSettings()
DataAnnotationQueryExpression	CellposeTrainingAlgorithm.getLabelDataAnnotation()
CellposeModel	CellposeAlgorithm.getModel()
int	CellposeTrainingAlgorithm.getNumEpochs()
OptionalPythonEnvironment	CellposeTrainingAlgorithm.getOverrideEnvironment()
OptionalPythonEnvironment	CellposeAlgorithm.getOverrideEnvironment()
CellposePretrainedModel	CellposeTrainingAlgorithm.getPretrainedModel()
CellposeSegmentationOutputSettings	CellposeAlgorithm.getSegmentationOutputSettings()
CellposeSegmentationThresholdSettings	CellposeAlgorithm.getThresholdParameters()
CellposeTrainingTweaksSettings	CellposeTrainingAlgorithm.getTweaksSettings()
boolean	CellposeTrainingAlgorithm.isCleanUpAfterwards()
boolean	CellposeAlgorithm.isCleanUpAfterwards()
boolean	CellposeTrainingAlgorithm.isEnable3DSegmentation()
boolean	CellposeAlgorithm.isEnable3DSegmentation()
boolean	CellposeTrainingAlgorithm.isTrainSizeModel()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.cellpose.algorithms.deprecated

Classes in org.hkijena.jipipe.extensions.cellpose.algorithms.deprecated with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CellposeAlgorithm_Old Deprecated. New implementation will be CellposeAlgorithm2 that is based around the Cellpose CLI
class	CellposeTrainingAlgorithm_Old Deprecated.

Methods in org.hkijena.jipipe.extensions.cellpose.algorithms.deprecated with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	CellposeTrainingAlgorithm_Old.getBatchSize() Deprecated.
int	CellposeTrainingAlgorithm_Old.getDiameter() Deprecated.
OptionalDoubleParameter	CellposeAlgorithm_Old.getDiameter() Deprecated.
OptionalAnnotationNameParameter	CellposeAlgorithm_Old.getDiameterAnnotation() Deprecated.
CellposeSegmentationEnhancementSettings_Old	CellposeAlgorithm_Old.getEnhancementParameters() Deprecated.
CellposeGPUSettings	CellposeTrainingAlgorithm_Old.getGpuSettings() Deprecated.
DataAnnotationQueryExpression	CellposeTrainingAlgorithm_Old.getLabelDataAnnotation() Deprecated.
double	CellposeTrainingAlgorithm_Old.getLearningRate() Deprecated.
int	CellposeTrainingAlgorithm_Old.getMinTrainMasks() Deprecated.
CellposeSegmentationModelSettings_Old	CellposeAlgorithm_Old.getModelParameters() Deprecated.
OptionalIntegerParameter	CellposeTrainingAlgorithm_Old.getNuclearChannel() Deprecated.
int	CellposeTrainingAlgorithm_Old.getNumEpochs() Deprecated.
CellposeSegmentationOutputSettings_Old	CellposeAlgorithm_Old.getOutputParameters() Deprecated.
OptionalPythonEnvironment	CellposeTrainingAlgorithm_Old.getOverrideEnvironment() Deprecated.
OptionalPythonEnvironment	CellposeAlgorithm_Old.getOverrideEnvironment() Deprecated.
CellposeSegmentationPerformanceSettings_Old	CellposeAlgorithm_Old.getPerformanceParameters() Deprecated.
CellposePretrainedModel	CellposeTrainingAlgorithm_Old.getPretrainedModel() Deprecated.
OptionalIntegerParameter	CellposeTrainingAlgorithm_Old.getSegmentedChannel() Deprecated.
CellposeSegmentationThresholdSettings_Old	CellposeAlgorithm_Old.getThresholdParameters() Deprecated.
double	CellposeTrainingAlgorithm_Old.getWeightDecay() Deprecated.
boolean	CellposeTrainingAlgorithm_Old.isCleanUpAfterwards() Deprecated.
boolean	CellposeAlgorithm_Old.isCleanUpAfterwards() Deprecated.
boolean	CellposeTrainingAlgorithm_Old.isConcatenateDownsampledLayers() Deprecated.
boolean	CellposeTrainingAlgorithm_Old.isEnable3DSegmentation() Deprecated.
boolean	CellposeAlgorithm_Old.isEnable3DSegmentation() Deprecated.
boolean	CellposeTrainingAlgorithm_Old.isGenerateConnectedComponents() Deprecated.
boolean	CellposeTrainingAlgorithm_Old.isTrainSizeModel() Deprecated.
boolean	CellposeTrainingAlgorithm_Old.isUseResidualConnections() Deprecated.
boolean	CellposeTrainingAlgorithm_Old.isUseStyleVector() Deprecated.

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.cellpose.compat

Classes in org.hkijena.jipipe.extensions.cellpose.compat with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CellposeModelImageJExporter
class	CellposeModelImageJImporter
class	CellposeSizeModelImageJExporter
class	CellposeSizeModelImageJImporter

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.cellpose.datatypes

Classes in org.hkijena.jipipe.extensions.cellpose.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CellposeModelData Wrapper around Cellpose models
class	CellposeSizeModelData Wrapper around Cellpose models

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.cellpose.installers

Classes in org.hkijena.jipipe.extensions.cellpose.installers with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CellposeEasyInstaller
class	MinicondaCellposeEnvInstaller
class	MinicondaCellposeGPUEnvInstaller
class	PortableCellposeEnvInstaller
class	PortableCellposeGPUEnvInstaller

Methods in org.hkijena.jipipe.extensions.cellpose.installers with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	MinicondaCellposeGPUEnvInstaller.Configuration.getCudaToolkitVersion()
String	PortableCellposeGPUEnvInstaller.Configuration.getPyTorchPipPackage()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.cellpose.parameters

Methods in org.hkijena.jipipe.extensions.cellpose.parameters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalDoubleParameter	CellposeSegmentationTweaksSettings.getAnisotropy()
int	CellposeTrainingTweaksSettings.getBatchSize()
double	CellposeSegmentationThresholdSettings.getCellProbabilityThreshold()
double	CellposeSegmentationThresholdSettings.getFlowThreshold()
OptionalIntegerParameter	CellposeGPUSettings.getGpuDevice()
double	CellposeTrainingTweaksSettings.getLearningRate()
int	CellposeTrainingTweaksSettings.getMinTrainMasks()
OptionalIntegerParameter	CellposeChannelSettings.getNuclearChannel()
OptionalIntegerParameter	CellposeChannelSettings.getSegmentedChannel()
OptionalDoubleParameter	CellposeSegmentationThresholdSettings.getStitchThreshold()
double	CellposeTrainingTweaksSettings.getWeightDecay()
boolean	CellposeChannelSettings.isAllChannels()
boolean	CellposeTrainingTweaksSettings.isConcatenateDownsampledLayers()
boolean	CellposeSegmentationTweaksSettings.isDisableResample()
boolean	CellposeGPUSettings.isEnableGPU()
boolean	CellposeSegmentationThresholdSettings.isExcludeOnEdges()
boolean	CellposeTrainingTweaksSettings.isGenerateConnectedComponents()
boolean	CellposeSegmentationTweaksSettings.isInterpolate()
boolean	CellposeChannelSettings.isInvert()
boolean	CellposeSegmentationTweaksSettings.isNetAverage()
boolean	CellposeSegmentationTweaksSettings.isNormalize()
boolean	CellposeSegmentationOutputSettings.isOutputFlowsD()
boolean	CellposeSegmentationOutputSettings.isOutputFlowsXY()
boolean	CellposeSegmentationOutputSettings.isOutputFlowsZ()
boolean	CellposeSegmentationOutputSettings.isOutputLabels()
boolean	CellposeSegmentationOutputSettings.isOutputProbabilities()
boolean	CellposeSegmentationOutputSettings.isOutputROI()
boolean	CellposeTrainingTweaksSettings.isUseResidualConnections()
boolean	CellposeTrainingTweaksSettings.isUseStyleVector()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.cellpose.parameters.deprecated

Methods in org.hkijena.jipipe.extensions.cellpose.parameters.deprecated with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalDoubleParameter	CellposeSegmentationEnhancementSettings_Old.getAnisotropy() Deprecated.
int	CellposeSegmentationPerformanceSettings_Old.getBatchSize() Deprecated.
double	CellposeSegmentationThresholdSettings_Old.getCellProbabilityThreshold() Deprecated.
double	CellposeSegmentationThresholdSettings_Old.getFlowThreshold() Deprecated.
double	CellposeSegmentationModelSettings_Old.getMeanDiameter() Deprecated.
int	CellposeSegmentationThresholdSettings_Old.getMinSize() Deprecated.
CellposeModel	CellposeSegmentationModelSettings_Old.getModel() Deprecated.
double	CellposeSegmentationThresholdSettings_Old.getStitchThreshold() Deprecated.
double	CellposeSegmentationPerformanceSettings_Old.getTileOverlap() Deprecated.
boolean	CellposeSegmentationEnhancementSettings_Old.isAugment() Deprecated.
boolean	CellposeSegmentationModelSettings_Old.isEnableGPU() Deprecated.
boolean	CellposeSegmentationEnhancementSettings_Old.isInterpolate() Deprecated.
boolean	CellposeSegmentationEnhancementSettings_Old.isNetAverage() Deprecated.
boolean	CellposeSegmentationEnhancementSettings_Old.isNormalize() Deprecated.
boolean	CellposeSegmentationOutputSettings_Old.isOutputFlows() Deprecated.
boolean	CellposeSegmentationOutputSettings_Old.isOutputLabels() Deprecated.
boolean	CellposeSegmentationOutputSettings_Old.isOutputProbabilities() Deprecated.
boolean	CellposeSegmentationOutputSettings_Old.isOutputROI() Deprecated.
boolean	CellposeSegmentationOutputSettings_Old.isOutputStyles() Deprecated.
boolean	CellposeSegmentationPerformanceSettings_Old.isResample() Deprecated.
boolean	CellposeSegmentationPerformanceSettings_Old.isTile() Deprecated.

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.clij2

Methods in org.hkijena.jipipe.extensions.clij2 with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ImageJCalibrationMode	CLIJSettings.ContrastEnhancerSettings.getCalibrationMode()
JIPipeDynamicParameterCollection	CLIJCommandNode.getClijParameters()
CLIJSettings.ContrastEnhancerSettings	CLIJSettings.getContrastEnhancerSettings()
double	CLIJSettings.ContrastEnhancerSettings.getCustomMax()
double	CLIJSettings.ContrastEnhancerSettings.getCustomMin()
int	CLIJSettings.getDevice()
boolean	CLIJSettings.ContrastEnhancerSettings.isApplyToAllPlanes()
boolean	CLIJSettings.isAutoCalibrateAfterPulling()
boolean	CLIJSettings.ContrastEnhancerSettings.isDuplicateImage()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.clij2.algorithms

Classes in org.hkijena.jipipe.extensions.clij2.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	Clij2ExecuteKernelIterating
class	Clij2ExecuteKernelSimpleIterating
class	Clij2PullAlgorithm
class	Clij2PushAlgorithm

Methods in org.hkijena.jipipe.extensions.clij2.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	Clij2ExecuteKernelIterating.getKernelFunction()
String	Clij2ExecuteKernelSimpleIterating.getKernelFunction()
OpenCLKernelScript	Clij2ExecuteKernelIterating.getKernelScript()
OpenCLKernelScript	Clij2ExecuteKernelSimpleIterating.getKernelScript()
PythonScript	Clij2ExecuteKernelIterating.getPreprocessingScript()
PythonScript	Clij2ExecuteKernelSimpleIterating.getPreprocessingScript()
JIPipeDynamicParameterCollection	Clij2ExecuteKernelIterating.getScriptParameters()
JIPipeDynamicParameterCollection	Clij2ExecuteKernelSimpleIterating.getScriptParameters()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.clij2.compat

Classes in org.hkijena.jipipe.extensions.clij2.compat with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CLIIJ2DataToImageWindowImageJExporter
class	CLIJ2DataFromImageWindowImageJImporter

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.clij2.datatypes

Classes in org.hkijena.jipipe.extensions.clij2.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CLIJImageData Contains a CLIJ image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.core.nodes

Classes in org.hkijena.jipipe.extensions.core.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	JIPipeCommentNode

Methods in org.hkijena.jipipe.extensions.core.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Color	JIPipeCommentNode.getBackgroundColor()
IconRef	JIPipeCommentNode.getIcon()
Color	JIPipeCommentNode.getTextColor()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.constants

Classes in org.hkijena.jipipe.extensions.expressions.constants with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BooleanFalseConstant
class	BooleanTrueConstant
class	NullConstant
class	NumericEulerConstant
class	NumericPiConstant
class	NumericTauConstant

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions

Classes in org.hkijena.jipipe.extensions.expressions.functions with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ContainsStringPredicateFunction
class	CopyNFunction
class	EvaluateFunction
class	ExpressionSequenceFunction
class	ForEachFunction
class	GlobStringPredicateFunction
class	IsNullFunction
class	LengthFunction
class	ParseJsonFunction
class	RemoveDuplicatesFunction
class	RunFunctionFunction
class	SequenceFunction
class	SummarizeVariablesFunction
class	VariableExistsFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.collections

Classes in org.hkijena.jipipe.extensions.expressions.functions.collections with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CreateArrayFunction
class	CreateMapFunction
class	CreatePairArrayFunction
class	FirstIndexOfFunction
class	GetFirstItemFunction
class	GetItemFunction
class	GetLastItemFunction
class	GetMapKeysFunction
class	GetMapValuesFunction
class	InvertFunction
class	LastIndexOfFunction
class	SliceFunction
class	SortAscendingArrayFunction
class	SortDescendingArrayFunction
class	SummarizeAnnotationsMapFunction
class	SummarizeMapFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.color

Classes in org.hkijena.jipipe.extensions.expressions.functions.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CreateHSBColorFunction
class	CreateLABColorFunction
class	CreateRGBColorFunction
class	FalseColorsFunction
class	HexToRGBFunction
class	HSBToLABFunction
class	HSBToRGBFunction
class	LABToHSBFunction
class	LABToRGBFunction
class	RGBToHexFunction
class	RGBToHSBFunction
class	RGBToLABFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.control

Classes in org.hkijena.jipipe.extensions.expressions.functions.control with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CaseFunction
class	IfElseExprFunction
class	IfElseFunction
class	SwitchCaseFunction
class	SwitchFunction
class	WhereFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.convert

Classes in org.hkijena.jipipe.extensions.expressions.functions.convert with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ToBooleanFunction
class	ToIntegerFunction
class	ToJsonFunction
class	ToNumber2Function
class	ToNumberFunction
class	ToStringFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.datetime

Classes in org.hkijena.jipipe.extensions.expressions.functions.datetime with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	GetDateDayFunction
class	GetDateMonthFunction
class	GetDateYearFunction
class	GetTimeHoursFunction
class	GetTimeMinutesFunction
class	GetTimeSecondsFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.filesystem

Classes in org.hkijena.jipipe.extensions.expressions.functions.filesystem with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	GetParentDirectoryFunction
class	GetPathNameFunction
class	IsDirectoryFunction
class	IsFileFunction
class	PathCombineFunction
class	PathExistsFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.functions

Classes in org.hkijena.jipipe.extensions.expressions.functions.functions with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DefineUserFunction
class	EvaluateUserFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.math

Classes in org.hkijena.jipipe.extensions.expressions.functions.math with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ClampFunction
class	DoubleToStringFunction
class	PercentageFunction
class	RandomFunction
class	RoundToDecimalsFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.quantities

Classes in org.hkijena.jipipe.extensions.expressions.functions.quantities with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	QuantityConvertFunction
class	QuantityGetUnitFunction
class	QuantityGetValueFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.statistics

Classes in org.hkijena.jipipe.extensions.expressions.functions.statistics with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AccumulateFunction
class	CumulativeTransformArrayFunction
class	HistogramFunction
class	HistogramThresholdHuang
class	HistogramThresholdImageJDefault
class	HistogramThresholdImageJIsoData
class	HistogramThresholdIntermodes
class	HistogramThresholdIsoData
class	HistogramThresholdLi
class	HistogramThresholdMaxEntropy
class	HistogramThresholdMean
class	HistogramThresholdMinError
class	HistogramThresholdMinimum
class	HistogramThresholdMoments
class	HistogramThresholdOtsu
class	HistogramThresholdPercentile
class	HistogramThresholdRenyi
class	HistogramThresholdShanbhag
class	HistogramThresholdTriangle
class	HistogramThresholdYen
class	PercentileFunction
class	TransformArrayFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.string

Classes in org.hkijena.jipipe.extensions.expressions.functions.string with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	EqualsStringPredicateFunction
class	ExtractRegexMatchesFunction
class	RegexStringPredicateFunction
class	StringEndsWithPredicateFunction
class	StringFirstIndexOfFunction
class	StringFormatFunction
class	StringJoinFunction
class	StringLastIndexOfFunction
class	StringRegexReplaceFunction
class	StringReplaceFunction
class	StringSliceBeforeFunction
class	StringSliceFunction
class	StringSplitFunction
class	StringStartsWithPredicateFunction
class	StringToLowerCaseFunction
class	StringToUpperCaseFunction
class	StringTruncateFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.util

Classes in org.hkijena.jipipe.extensions.expressions.functions.util with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	PrintFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.functions.variables

Classes in org.hkijena.jipipe.extensions.expressions.functions.variables with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	GetVariableFunction
class	GetVariableKeysFunction
class	GetVariablesAsMapFunction
class	GetVariableValuesFunction
class	HasVariableFunction
class	SetMissingVariableFunction
class	SetVariableFunction
class	SetVariableIfFunction
class	SetVariablesFunction

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.expressions.operators

Classes in org.hkijena.jipipe.extensions.expressions.operators with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AdditionFunctionOperator
class	ContainsOperator Operator that tests if the left string is contained in the right string
class	ContainsOperator2 Operator that tests if the left string is contained in the right string
class	ElementAccessOperator
class	EqualityPredicateOperator
class	InequalityPredicateOperator
class	LogicalAndOperator
class	LogicalNotOperator
class	LogicalOrOperator
class	LogicalXOrOperator
class	NumericDivideFunctionOperator
class	NumericExponentFunctionOperator
class	NumericGreaterThanOrEqualPredicateOperator
class	NumericGreaterThanPredicateOperator
class	NumericLessThanOrEqualPredicateOperator
class	NumericLessThanPredicateOperator
class	NumericModuloFunctionOperator
class	NumericMultiplyFunctionOperator
class	PairOperator Operator that is used to make different statements The return value is the right statement
class	ResolveVariableOperator
class	StatementOperator Operator that is used to make different statements The return value is the right statement
class	SubtractionFunctionOperator
class	VariableExistsOperator

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.filesystem

Methods in org.hkijena.jipipe.extensions.filesystem with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
boolean	FilesystemExtensionSettings.isAutoLabelOutputWithFileName()
boolean	FilesystemExtensionSettings.isRelativizePaths()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.filesystem.algorithms

Classes in org.hkijena.jipipe.extensions.filesystem.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AnnotateWithPathProperties
class	AnnotationTableToPaths Filters input files
class	AnnotationToPath Filters input files
class	ConcatenateByParameter Applies subfolder navigation to each input folder
class	ConcatenatePaths Applies subfolder navigation to each input folder
class	ConvertDataToOutputPath Applies subfolder navigation to each input folder
class	CopyPath Applies subfolder navigation to each input folder
class	CreateDirectory Applies subfolder navigation to each input folder
class	ExportData
class	ExportDataByParameter
class	ExportDataTable
class	ExportDataTableByParameter
class	ExtractFileName Applies subfolder navigation to each input folder
class	ExtractParent Applies subfolder navigation to each input folder
class	FilterPaths Filters input files
class	ImportDataRowFolder
class	ImportDataTableArchive
class	ImportDataTableDirectory
class	ListFiles Algorithm that lists files in each folder
class	ListSubfolders Algorithms that lists the sub folders for each input folder
class	ModifyPath
class	RelativizeByParameter Applies subfolder navigation to each input folder
class	RelativizePaths Applies subfolder navigation to each input folder
class	RenameByString Applies subfolder navigation to each input folder
class	SimpleFileAnnotationGenerator Generates annotations from filenames
class	SimpleFolderAnnotationGenerator Algorithm that generates annotations from folder names
class	SimplePathAnnotationGenerator Algorithm that generates annotations from folder names

Methods in org.hkijena.jipipe.extensions.filesystem.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
AnnotationQueryExpression	AnnotationToPath.getAnnotationExpression()
JIPipeTextAnnotationMergeMode	SimplePathAnnotationGenerator.getAnnotationMergeStrategy()
StringAndStringPairParameter.List	ImportDataRowFolder.getAnnotations()
TableColumnSourceExpressionParameter	AnnotationTableToPaths.getColumn()
JIPipeDataAnnotationMergeMode	ImportDataTableDirectory.getDataAnnotationMergeMode()
JIPipeDataAnnotationMergeMode	ImportDataTableArchive.getDataAnnotationMergeMode()
JIPipeDataInfoRef	ImportDataRowFolder.getDataType()
JIPipeDataByMetadataExporter	ExportData.getExporter()
JIPipeDataByMetadataExporter	ExportDataByParameter.getExporter()
PathQueryExpression	ModifyPath.getExpression()
OptionalAnnotationNameParameter	AnnotateWithPathProperties.getFileNameAnnotation()
PathQueryExpression	FilterPaths.getFilters()
PathQueryExpression	ListFiles.getFilters()
PathQueryExpression	ListSubfolders.getFilters()
String	SimpleFolderAnnotationGenerator.getGeneratedAnnotation()
String	SimplePathAnnotationGenerator.getGeneratedAnnotation()
String	SimpleFileAnnotationGenerator.getGeneratedAnnotation()
String	ImportDataTableArchive.getInternalPath()
OptionalAnnotationNameParameter	AnnotateWithPathProperties.getLastModifiedTime()
int	ExtractParent.getOrder()
Path	ExportDataByParameter.getOutputDirectory()
Path	ExportDataTableByParameter.getOutputDirectory()
Path	RelativizeByParameter.getParentPath()
OptionalAnnotationNameParameter	AnnotateWithPathProperties.getParentPathAnnotation()
String	RenameByString.getPathName()
OptionalAnnotationNameParameter	AnnotateWithPathProperties.getSizeAnnotation()
String	ListFiles.getSubFolder()
String	ListSubfolders.getSubFolder()
Path	ConcatenateByParameter.getSubPath()
JIPipeTextAnnotationMergeMode	ImportDataTableDirectory.getTextAnnotationMergeMode()
JIPipeTextAnnotationMergeMode	ImportDataTableArchive.getTextAnnotationMergeMode()
OptionalAnnotationNameParameter	AnnotateWithPathProperties.getTypeAnnotation()
boolean	ModifyPath.isAccessAnnotations()
boolean	CopyPath.isAppendDirectoryNameToTarget()
boolean	SimplePathAnnotationGenerator.isFullPath()
boolean	ImportDataTableDirectory.isIgnoreImportedDataAnnotations()
boolean	ImportDataTableArchive.isIgnoreImportedDataAnnotations()
boolean	ImportDataTableDirectory.isIgnoreImportedTextAnnotations()
boolean	ImportDataTableArchive.isIgnoreImportedTextAnnotations()
boolean	ImportDataTableDirectory.isIgnoreInputDataAnnotations()
boolean	ImportDataTableArchive.isIgnoreInputDataAnnotations()
boolean	ImportDataTableDirectory.isIgnoreInputTextAnnotations()
boolean	ImportDataTableArchive.isIgnoreInputTextAnnotations()
boolean	FilterPaths.isOutputFiles()
boolean	FilterPaths.isOutputFolders()
boolean	FilterPaths.isOutputNonExisting()
boolean	ListFiles.isRecursive()
boolean	ListSubfolders.isRecursive()
boolean	ListFiles.isRecursiveFollowsLinks()
boolean	ListSubfolders.isRecursiveFollowsLinks()
boolean	ExportDataByParameter.isRelativeToProjectDir()
boolean	ExportDataTableByParameter.isRelativeToProjectDir()
boolean	SimplePathAnnotationGenerator.isRemoveExtensions()
boolean	CopyPath.isSkipExisting()
boolean	CopyPath.isSkipInvalid()
boolean	ExportData.isSplitBySlotName()
boolean	ExportDataByParameter.isSplitBySlotName()
boolean	CreateDirectory.isWithParents()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.filesystem.compat

Classes in org.hkijena.jipipe.extensions.filesystem.compat with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	PathDataFromTableImageJImporter
class	PathDataToTableImageJExporter

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.filesystem.datasources

Classes in org.hkijena.jipipe.extensions.filesystem.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DownloadFilesDataSource
class	FileDataSource Provides an input file
class	FileListDataSource Provides an input file
class	FolderDataSource Provides an input folder
class	FolderListDataSource Provides an input folder
class	OutputFolderDataSource
class	PathDataSource Provides an input file
class	PathFromUserDataSource
class	PathListDataSource Provides an input folder
class	TemporaryFileDataSource
class	TemporaryFolderDataSource

Methods in org.hkijena.jipipe.extensions.filesystem.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
void	PathListDataSource.convertPathsToAbsolute()
void	FileListDataSource.convertPathsToAbsolute()
void	FolderListDataSource.convertPathsToAbsolute()
void	PathListDataSource.convertPathsToRelative()
void	FileListDataSource.convertPathsToRelative()
void	FolderListDataSource.convertPathsToRelative()
String	TemporaryFolderDataSource.getBaseName()
Path	FileDataSource.getFileName()
PathList	FileListDataSource.getFiles()
Path	FolderDataSource.getFolderPath()
PathList	FolderListDataSource.getFolderPaths()
Path	PathDataSource.getPath()
PathIOMode	PathFromUserDataSource.getPathIOMode()
PathList	PathListDataSource.getPaths()
PathType	PathFromUserDataSource.getPathType()
String	TemporaryFileDataSource.getPrefix()
String	TemporaryFileDataSource.getSuffix()
StringList	DownloadFilesDataSource.getUrls()
boolean	PathFromUserDataSource.isMultiple()
boolean	PathDataSource.isNeedsToExist()
boolean	FolderDataSource.isNeedsToExist()
boolean	FileDataSource.isNeedsToExist()
boolean	TemporaryFolderDataSource.isUseScratchDirectory()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.filesystem.dataypes

Classes in org.hkijena.jipipe.extensions.filesystem.dataypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	FileData Data containing a file
class	FolderData Data that stores a folder
class	PathData Encapsulates a Path

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.forms.algorithms

Classes in org.hkijena.jipipe.extensions.forms.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BooleanFormGeneratorAlgorithm
class	DoubleFormGeneratorAlgorithm
class	EnumFormGeneratorAlgorithm
class	GroupHeaderFormGeneratorAlgorithm
class	IntegerFormGeneratorAlgorithm
class	IteratingFormProcessorAlgorithm
class	MergingFormProcessorAlgorithm
class	PathFormGeneratorAlgorithm
class	SimpleIteratingFormProcessorAlgorithm
class	StringFormGeneratorAlgorithm

Methods in org.hkijena.jipipe.extensions.forms.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeMergingAlgorithmDataBatchGenerationSettings	MergingFormProcessorAlgorithm.getDataBatchGenerationSettings()
JIPipeSimpleIteratingAlgorithmDataBatchGenerationSettings	SimpleIteratingFormProcessorAlgorithm.getDataBatchGenerationSettings()
JIPipeMergingAlgorithmDataBatchGenerationSettings	IteratingFormProcessorAlgorithm.getDataBatchGenerationSettings()
FormData	SimpleFormGeneratorAlgorithm.getFormData()
String	MergingFormProcessorAlgorithm.getTabAnnotation()
String	SimpleIteratingFormProcessorAlgorithm.getTabAnnotation()
String	IteratingFormProcessorAlgorithm.getTabAnnotation()
boolean	IteratingFormProcessorAlgorithm.isRestoreAnnotations()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.forms.datatypes

Classes in org.hkijena.jipipe.extensions.forms.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BooleanFormData
class	DoubleFormData
class	EnumFormData
class	FormData Base class for any form data.
class	GroupHeaderFormData
class	IntegerFormData
class	PathFormData
class	StringFormData

Methods in org.hkijena.jipipe.extensions.forms.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
SingleAnnotationIOSettings	IntegerFormData.getAnnotationIOSettings()
SingleAnnotationIOSettings	DoubleFormData.getAnnotationIOSettings()
SingleAnnotationIOSettings	EnumFormData.getAnnotationIOSettings()
SingleAnnotationIOSettings	BooleanFormData.getAnnotationIOSettings()
SingleAnnotationIOSettings	StringFormData.getAnnotationIOSettings()
SingleAnnotationIOSettings	PathFormData.getAnnotationIOSettings()
HTMLText	ParameterFormData.getDescription()
StringList	PathFormData.getExtensions()
OptionalStringParameter	BooleanFormData.getFalseString()
PathIOMode	PathFormData.getIoMode()
StringAndStringPairParameter.List	EnumFormData.getItems()
String	ParameterFormData.getName()
PathType	PathFormData.getPathType()
String	FormData.TabSettings.getTab()
OptionalAnnotationNameParameter	FormData.TabSettings.getTabAnnotation()
FormData.TabSettings	FormData.getTabSettings()
OptionalStringParameter	BooleanFormData.getTrueString()
DefaultExpressionParameter	IntegerFormData.getValidationExpression()
DefaultExpressionParameter	DoubleFormData.getValidationExpression()
StringQueryExpression	StringFormData.getValidationExpression()
StringQueryExpression	PathFormData.getValidationExpression()
int	IntegerFormData.getValue()
double	DoubleFormData.getValue()
String	EnumFormData.getValue()
boolean	BooleanFormData.getValue()
String	StringFormData.getValue()
Path	PathFormData.getValue()
boolean	ParameterFormData.isShowName()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.forms.utils

Methods in org.hkijena.jipipe.extensions.forms.utils with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeTextAnnotationMergeMode	SingleAnnotationIOSettings.getAnnotationMergeStrategy()
OptionalAnnotationNameParameter	SingleAnnotationIOSettings.getInputAnnotation()
OptionalAnnotationNameParameter	SingleAnnotationIOSettings.getOutputAnnotation()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijmultitemplatematching

Classes in org.hkijena.jipipe.extensions.ijmultitemplatematching with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	MultiTemplateMatchingAlgorithm

Methods in org.hkijena.jipipe.extensions.ijmultitemplatematching with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
void	MultiTemplateMatchingAlgorithm.generateRotations(JIPipeWorkbench workbench)
OptionalColorParameter	MultiTemplateMatchingAlgorithm.getAssembleTemplatesBackground()
OptionalDataInfoRefParameter	MultiTemplateMatchingAlgorithm.getAssembleTemplatesOutput()
int	MultiTemplateMatchingAlgorithm.getExpectedNumberOfObjects()
double	MultiTemplateMatchingAlgorithm.getMultiObjectMaximumBoundingBoxOverlap()
double	MultiTemplateMatchingAlgorithm.getMultiObjectScoreThreshold()
IntegerRange	MultiTemplateMatchingAlgorithm.getRotateTemplate()
TemplateMatchingMethod	MultiTemplateMatchingAlgorithm.getTemplateMatchingMethod()
boolean	MultiTemplateMatchingAlgorithm.isAssembleTemplates()
boolean	MultiTemplateMatchingAlgorithm.isFlipTemplateHorizontally()
boolean	MultiTemplateMatchingAlgorithm.isFlipTemplateVertically()
boolean	MultiTemplateMatchingAlgorithm.isRestrictToROI()
boolean	MultiTemplateMatchingAlgorithm.isWithNonMaximaSuppression()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijtrackmate.datatypes

Classes in org.hkijena.jipipe.extensions.ijtrackmate.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ModelData
class	SpotDetectorData
class	SpotsCollectionData
class	SpotTrackerData
class	TrackCollectionData

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijtrackmate.nodes.converters

Classes in org.hkijena.jipipe.extensions.ijtrackmate.nodes.converters with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ConvertSpotsToRoiNode
class	ConvertTracksToRoiNode

Methods in org.hkijena.jipipe.extensions.ijtrackmate.nodes.converters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
NamedTextAnnotationGeneratorExpression.List	ConvertTracksToRoiNode.getAnnotationGenerator()
OptionalDefaultExpressionParameter	ConvertSpotsToRoiNode.getFillColor()
OptionalDefaultExpressionParameter	ConvertTracksToRoiNode.getFillColor()
OptionalDefaultExpressionParameter	ConvertSpotsToRoiNode.getLineColor()
OptionalDefaultExpressionParameter	ConvertTracksToRoiNode.getLineColor()
OptionalDefaultExpressionParameter	ConvertSpotsToRoiNode.getLineWidth()
OptionalDefaultExpressionParameter	ConvertTracksToRoiNode.getLineWidth()
OptionalDefaultExpressionParameter	ConvertSpotsToRoiNode.getRoiName()
OptionalDefaultExpressionParameter	ConvertTracksToRoiNode.getRoiName()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijtrackmate.nodes.detectors

Methods in org.hkijena.jipipe.extensions.ijtrackmate.nodes.detectors with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeDynamicParameterCollection	CreateSpotDetectorNode.getParameters()
JIPipeDynamicParameterCollection	CreateSpotTrackerNode.getParameters()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijtrackmate.nodes.spots

Classes in org.hkijena.jipipe.extensions.ijtrackmate.nodes.spots with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	MeasureSpotsNode
class	MergeSpotsNode
class	SplitSpotsNode
class	SpotDetectorNode
class	SpotFilterNode
class	SpotsToRGBNode

Methods in org.hkijena.jipipe.extensions.ijtrackmate.nodes.spots with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
NamedTextAnnotationGeneratorExpression.List	SplitSpotsNode.getAnnotationGenerator()
CustomExpressionVariablesParameter	SpotFilterNode.getCustomVariables()
CustomExpressionVariablesParameter	SplitSpotsNode.getCustomVariables()
DefaultExpressionParameter	SpotFilterNode.getFilter()
double	SpotsToRGBNode.getMagnification()
SpotDrawer	SpotsToRGBNode.getSpotDrawer()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijtrackmate.nodes.tracks

Classes in org.hkijena.jipipe.extensions.ijtrackmate.nodes.tracks with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	FollowSpotsPerTrackNode
class	MeasureBranchesNode
class	MeasureEdgesNode
class	MeasureTracksNode
class	MergeTracksNode
class	SplitTracksNode
class	TrackFilterNode
class	TrackingNode
class	TrackSchemeRendererNode
class	TracksToRGBNode

Methods in org.hkijena.jipipe.extensions.ijtrackmate.nodes.tracks with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
NamedTextAnnotationGeneratorExpression.List	SplitTracksNode.getAnnotationGenerator()
CustomExpressionVariablesParameter	TrackFilterNode.getCustomVariables()
DefaultExpressionParameter	TrackFilterNode.getFilter()
double	TracksToRGBNode.getMagnification()
int	FollowSpotsPerTrackNode.getMinHeight()
int	FollowSpotsPerTrackNode.getMinWidth()
TrackDrawer	TracksToRGBNode.getTrackDrawer()
OptionalAnnotationNameParameter	FollowSpotsPerTrackNode.getTrackIDAnnotation()
boolean	FollowSpotsPerTrackNode.isCropT()
boolean	FollowSpotsPerTrackNode.isCropXY()
boolean	FollowSpotsPerTrackNode.isCropZ()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijtrackmate.parameters

Methods in org.hkijena.jipipe.extensions.ijtrackmate.parameters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
SpotFeature	SpotFeatureFilterParameter.getFeature()
TrackFeature	TrackFeatureFilterParameter.getFeature()
SpotFeature	SpotFeaturePenaltyParameter.getFeature()
double	SpotFeaturePenaltyParameter.getPenalty()
double	SpotFeatureFilterParameter.getValue()
double	TrackFeatureFilterParameter.getValue()
boolean	SpotFeatureFilterParameter.isAbove()
boolean	TrackFeatureFilterParameter.isAbove()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijtrackmate.settings

Methods in org.hkijena.jipipe.extensions.ijtrackmate.settings with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
SpotDrawer	ImageViewerUISpotsDisplaySettings.getSpotDrawer()
TrackDrawer	ImageViewerUITracksDisplaySettings.getTrackDrawer()
boolean	ImageViewerUISpotsDisplaySettings.isShowSpots()
boolean	ImageViewerUITracksDisplaySettings.isShowTracks()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijtrackmate.utils

Methods in org.hkijena.jipipe.extensions.ijtrackmate.utils with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
SpotFeature	SpotDrawer.LabelSettings.getDrawnFeature()
int	TrackDrawer.getFadeTrackRange()
OptionalColorParameter	DrawerLabelSettings.getLabelBackground()
Color	DrawerLabelSettings.getLabelForeground()
SpotDrawer.LabelSettings	SpotDrawer.getLabelSettings()
int	DrawerLabelSettings.getLabelSize()
Color	TrackDrawer.getStrokeColor()
Color	SpotDrawer.getStrokeColor()
EdgeFeature	TrackDrawer.getStrokeColorEdgeFeature()
SpotFeature	SpotDrawer.getStrokeColorFeature()
TrackDrawer.StrokeColorMode	TrackDrawer.getStrokeColorMode()
TrackFeature	TrackDrawer.getStrokeColorTrackFeature()
int	TrackDrawer.getStrokeWidth()
int	SpotDrawer.getStrokeWidth()
DisplaySettings.TrackDisplayMode	TrackDrawer.getTrackDisplayMode()
boolean	DrawerLabelSettings.isDrawLabels()
boolean	SpotDrawer.LabelSettings.isDrawName()
boolean	SpotDrawer.isFillSpots()
boolean	SpotDrawer.isUniformStrokeColor()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijweka.datatypes

Classes in org.hkijena.jipipe.extensions.ijweka.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	WekaModelData Wrapper around Cellpose models

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijweka.nodes

Classes in org.hkijena.jipipe.extensions.ijweka.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImportWekaModelFromFileAlgorithm
class	WekaClassification2DAlgorithm
class	WekaClassification3DAlgorithm
class	WekaTrainingLabels2DAlgorithm
class	WekaTrainingMask2DAlgorithm
class	WekaTrainingROI2DAlgorithm
class	WekaTrainingROI3DAlgorithm

Methods in org.hkijena.jipipe.extensions.ijweka.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
InputSlotMapParameterCollection	WekaTrainingROI3DAlgorithm.getClassAssignment()
InputSlotMapParameterCollection	WekaTrainingROI2DAlgorithm.getClassAssignment()
WekaClassifierSettings	WekaTrainingROI3DAlgorithm.getClassifierSettings()
WekaClassifierSettings	WekaTrainingROI2DAlgorithm.getClassifierSettings()
WekaClassifierSettings	WekaTrainingLabels2DAlgorithm.getClassifierSettings()
WekaClassifierSettings	WekaTrainingMask2DAlgorithm.getClassifierSettings()
WekaFeature3DSettings	WekaTrainingROI3DAlgorithm.getFeatureSettings()
WekaFeature2DSettings	WekaTrainingROI2DAlgorithm.getFeatureSettings()
WekaFeature2DSettings	WekaTrainingLabels2DAlgorithm.getFeatureSettings()
WekaFeature2DSettings	WekaTrainingMask2DAlgorithm.getFeatureSettings()
OptionalIntegerParameter	WekaClassification2DAlgorithm.getNumThreads()
OptionalIntegerParameter	WekaClassification3DAlgorithm.getNumThreads()
WekaTiling3DSettings	WekaClassification3DAlgorithm.getTilingParameters()
WekaTiling2DSettings	WekaClassification2DAlgorithm.getTilingSettings()
boolean	WekaClassification2DAlgorithm.isOutputProbabilityMaps()
boolean	WekaClassification3DAlgorithm.isOutputProbabilityMaps()
boolean	ImportWekaModelFromFileAlgorithm.isProcessing3D()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijweka.parameters

Methods in org.hkijena.jipipe.extensions.ijweka.parameters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
WekaClassifierParameter	WekaClassifierSettings.getClassifier()
boolean	WekaClassifierSettings.isBalanceClasses()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.ijweka.parameters.collections

Methods in org.hkijena.jipipe.extensions.ijweka.parameters.collections with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
BorderMode	WekaTiling2DSettings.getBorderMode()
float	WekaFeature2DSettings.getMaxSigma()
float	WekaFeature3DSettings.getMaxSigma()
int	WekaFeature2DSettings.getMembranePatchSize()
int	WekaFeature3DSettings.getMembranePatchSize()
int	WekaFeature2DSettings.getMembraneSize()
int	WekaFeature3DSettings.getMembraneSize()
float	WekaFeature2DSettings.getMinSigma()
float	WekaFeature3DSettings.getMinSigma()
int	WekaTiling2DSettings.getOverlapX()
int	WekaTiling2DSettings.getOverlapY()
int	WekaTiling2DSettings.getTileSizeX()
int	WekaTiling3DSettings.getTileSizeX()
int	WekaTiling2DSettings.getTileSizeY()
int	WekaTiling3DSettings.getTileSizeY()
int	WekaTiling3DSettings.getTileSizeZ()
WekaFeatureSet2D	WekaFeature2DSettings.getTrainingFeatures()
WekaFeatureSet3D	WekaFeature3DSettings.getTrainingFeatures()
boolean	WekaTiling2DSettings.isApplyTiling()
boolean	WekaTiling3DSettings.isApplyTiling()
boolean	WekaFeature2DSettings.isUseNeighbors()
boolean	WekaFeature3DSettings.isUseNeighbors()
boolean	WekaTiling2DSettings.isUseWekaNativeTiling()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagej2

Methods in org.hkijena.jipipe.extensions.imagej2 with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeDynamicParameterCollection	ImageJ2OpNode.getModuleParameters()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagej2.algorithms

Classes in org.hkijena.jipipe.extensions.imagej2.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CreateIJ2OutOfBoundsFactoryAlgorithm
class	CreateIJ2ShapeAlgorithm

Methods in org.hkijena.jipipe.extensions.imagej2.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ImageJ2OutOfBoundsFactoryData	CreateIJ2OutOfBoundsFactoryAlgorithm.getFactoryData()
JIPipeDataInfoRef	CreateIJ2OutOfBoundsFactoryAlgorithm.getFactoryType()
ImageJ2ShapeData	CreateIJ2ShapeAlgorithm.getShapeData()
JIPipeDataInfoRef	CreateIJ2ShapeAlgorithm.getShapeType()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagej2.compat

Classes in org.hkijena.jipipe.extensions.imagej2.compat with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	IJ2DataFromImageWindowImageJImporter
class	IJ2DataToImageWindowImageJExporter

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagej2.datatypes

Classes in org.hkijena.jipipe.extensions.imagej2.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImageJ2DatasetData

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagej2.datatypes.outofbounds

Classes in org.hkijena.jipipe.extensions.imagej2.datatypes.outofbounds with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BorderImageJ2OutOfBoundsFactoryData
class	EmptyImageJ2OutOfBoundsFactory
class	ImageJ2OutOfBoundsFactoryData
class	MirrorImageJ2OutOfBoundsFactoryData
class	PeriodicImageJ2OutOfBoundsFactoryData

Methods in org.hkijena.jipipe.extensions.imagej2.datatypes.outofbounds with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OutOfBoundsMirrorFactory.Boundary	MirrorImageJ2OutOfBoundsFactoryData.getBoundary()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagej2.datatypes.outofbounds.constant

Classes in org.hkijena.jipipe.extensions.imagej2.datatypes.outofbounds.constant with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ByteConstantValueImageJ2OutOfBoundsFactoryData
class	DoubleConstantValueImageJ2OutOfBoundsFactoryData
class	FloatConstantValueImageJ2OutOfBoundsFactoryData
class	IntegerConstantValueImageJ2OutOfBoundsFactoryData
class	LongConstantValueImageJ2OutOfBoundsFactoryData
class	ShortConstantValueImageJ2OutOfBoundsFactoryData

Methods in org.hkijena.jipipe.extensions.imagej2.datatypes.outofbounds.constant with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
byte	ByteConstantValueImageJ2OutOfBoundsFactoryData.getValue()
int	IntegerConstantValueImageJ2OutOfBoundsFactoryData.getValue()
float	FloatConstantValueImageJ2OutOfBoundsFactoryData.getValue()
long	LongConstantValueImageJ2OutOfBoundsFactoryData.getValue()
double	DoubleConstantValueImageJ2OutOfBoundsFactoryData.getValue()
short	ShortConstantValueImageJ2OutOfBoundsFactoryData.getValue()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagej2.datatypes.shapes

Classes in org.hkijena.jipipe.extensions.imagej2.datatypes.shapes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CenteredRectangleImageJ2ShapeData
class	DiamondImageJ2ShapeData
class	DiamondTipsImageJ2ShapeData
class	EmptyImageJ2ShapeData
class	HorizontalLineImageJ2ShapeData
class	HyperSphereImageJ2ShapeData
class	ImageJ2ShapeData
class	PairOfPointsImageJ2ShapeData
class	PeriodicLineImageJ2ShapeData
class	RectangleImageJ2ShapeData

Methods in org.hkijena.jipipe.extensions.imagej2.datatypes.shapes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
IntegerList	PeriodicLineImageJ2ShapeData.getIncrements()
int	HorizontalLineImageJ2ShapeData.getLineDimension()
LongList	PairOfPointsImageJ2ShapeData.getOffset()
long	DiamondImageJ2ShapeData.getRadius()
long	DiamondTipsImageJ2ShapeData.getRadius()
long	HyperSphereImageJ2ShapeData.getRadius()
IntegerList	CenteredRectangleImageJ2ShapeData.getSpan()
int	RectangleImageJ2ShapeData.getSpan()
long	HorizontalLineImageJ2ShapeData.getSpan()
long	PeriodicLineImageJ2ShapeData.getSpan()
boolean	CenteredRectangleImageJ2ShapeData.isSkipCenter()
boolean	RectangleImageJ2ShapeData.isSkipCenter()
boolean	HorizontalLineImageJ2ShapeData.isSkipCenter()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1 with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	MacroWrapperAlgorithm An algorithm that wraps around an ImageJ macro

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1 with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ImageJMacro	MacroWrapperAlgorithm.getCode()
int	MacroWrapperAlgorithm.getExportDelay()
int	MacroWrapperAlgorithm.getImportDelay()
InputSlotMapParameterCollection	MacroWrapperAlgorithm.getInputToImageJExporters()
JIPipeDynamicParameterCollection	MacroWrapperAlgorithm.getMacroParameters()
OutputSlotMapParameterCollection	MacroWrapperAlgorithm.getOutputFromImageJImporters()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.analyze

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.analyze with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AnalyzeSkeleton2D3DAlgorithm
class	AnnotateByImageStatisticsExpressionAlgorithm Wrapper around RoiManager
class	FindParticles2D Converts a mask to ROI and ROI measurements
class	ImageStatisticsAlgorithm Wrapper around RoiManager
class	ImageStatisticsExpressionAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.analyze with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ExpressionTableColumnGeneratorProcessorParameterList	AnnotateByImageStatisticsExpressionAlgorithm.getAnnotations()
OptionalStringParameter	FindParticles2D.getAnnotationType()
ExpressionTableColumnGeneratorProcessorParameterList	ImageStatisticsExpressionAlgorithm.getColumns()
OptionalStringParameter	ImageStatisticsAlgorithm.getIndexAnnotation()
double	FindParticles2D.getMaxParticleCircularity()
double	FindParticles2D.getMaxParticleSize()
ImageStatisticsSetParameter	ImageStatisticsAlgorithm.getMeasurements()
double	FindParticles2D.getMinParticleCircularity()
double	FindParticles2D.getMinParticleSize()
Neighborhood2D	FindParticles2D.getNeighborhood()
AnalyzeSkeleton2D3DAlgorithm.OutputParameters	AnalyzeSkeleton2D3DAlgorithm.getOutputParameters()
AnalyzeSkeleton2D3DAlgorithm.CycleRemovalMethod	AnalyzeSkeleton2D3DAlgorithm.getPruneCyclesMethod()
AnalyzeSkeleton2D3DAlgorithm.EndRemovalMethod	AnalyzeSkeleton2D3DAlgorithm.getPruneEndsMethod()
ImageStatisticsSetParameter	FindParticles2D.getStatisticsParameters()
ImageROITargetArea	AnnotateByImageStatisticsExpressionAlgorithm.getTargetArea()
ImageROITargetArea	ImageStatisticsExpressionAlgorithm.getTargetArea()
boolean	ImageStatisticsExpressionAlgorithm.isApplyPerChannel()
boolean	ImageStatisticsAlgorithm.isApplyPerChannel()
boolean	ImageStatisticsExpressionAlgorithm.isApplyPerFrame()
boolean	ImageStatisticsAlgorithm.isApplyPerFrame()
boolean	ImageStatisticsExpressionAlgorithm.isApplyPerSlice()
boolean	ImageStatisticsAlgorithm.isApplyPerSlice()
boolean	FindParticles2D.isBlackBackground()
boolean	FindParticles2D.isExcludeEdges()
boolean	FindParticles2D.isIncludeHoles()
boolean	ImageStatisticsAlgorithm.isMeasureInPhysicalUnits()
boolean	FindParticles2D.isMeasureInPhysicalUnits()
boolean	AnalyzeSkeleton2D3DAlgorithm.OutputParameters.isOutputBranchTable()
boolean	AnalyzeSkeleton2D3DAlgorithm.OutputParameters.isOutputLargestShortestPaths()
boolean	AnalyzeSkeleton2D3DAlgorithm.OutputParameters.isOutputSkeletonLabels()
boolean	AnalyzeSkeleton2D3DAlgorithm.OutputParameters.isOutputSkeletonTable()
boolean	AnalyzeSkeleton2D3DAlgorithm.OutputParameters.isOutputTaggedSkeletons()
boolean	FindParticles2D.isSplitSlices()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.background

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.background with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	RollingBallBackgroundEstimator2DAlgorithm Wrapper around RankFilters

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.background with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
RollingBallBackgroundEstimator2DAlgorithm.BackgroundType	RollingBallBackgroundEstimator2DAlgorithm.getBackgroundType()
RollingBallBackgroundEstimator2DAlgorithm.Method	RollingBallBackgroundEstimator2DAlgorithm.getMethod()
double	RollingBallBackgroundEstimator2DAlgorithm.getRadius()
boolean	RollingBallBackgroundEstimator2DAlgorithm.isCorrectCorners()
boolean	RollingBallBackgroundEstimator2DAlgorithm.isPreSmoothing()
boolean	RollingBallBackgroundEstimator2DAlgorithm.isSeparateChannels()
boolean	RollingBallBackgroundEstimator2DAlgorithm.isSubtract()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.binary

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.binary with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BinarizeAlgorithm
class	BitwiseLogicalOperationAlgorithm
class	ConditionalInverterAlgorithm
class	ConnectedComponentsLabeling2DAlgorithm
class	ConnectedComponentsLabeling3DAlgorithm
class	ConvexifyAlgorithm
class	DistanceTransformWatershed2DAlgorithm Wrapper around EDM
class	KeepLargestRegionAlgorithm
class	RemoveLargestRegionAlgorithm
class	UltimateErodedPoints2DAlgorithm Wrapper around EDM
class	VolumeOpening2DAlgorithm
class	VolumeOpening3DAlgorithm
class	Voronoi2DAlgorithm Wrapper around EDM

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.binary with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DefaultExpressionParameter	ConditionalInverterAlgorithm.getCondition()
Neighborhood2D	ConnectedComponentsLabeling2DAlgorithm.getConnectivity()
Neighborhood2D	ConnectedComponentsLabeling3DAlgorithm.getConnectivity()
int	RemoveLargestRegionAlgorithm.getIterations()
LogicalOperation	BitwiseLogicalOperationAlgorithm.getLogicalOperation()
int	VolumeOpening3DAlgorithm.getMinPixels()
int	VolumeOpening2DAlgorithm.getMinPixels()
JIPipeDataInfoRef	ConnectedComponentsLabeling2DAlgorithm.getOutputType()
JIPipeDataInfoRef	ConnectedComponentsLabeling3DAlgorithm.getOutputType()
boolean	ConditionalInverterAlgorithm.isApplyPerSlice()
boolean	Voronoi2DAlgorithm.isBinarize()
boolean	BinarizeAlgorithm.isInvert()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.blur

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.blur with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BoxFilter2DAlgorithm Wrapper around ImageProcessor
class	BoxFilter3DAlgorithm Wrapper around GaussianBlur
class	GaussianBlur2DAlgorithm Wrapper around GaussianBlur
class	GaussianBlur3DAlgorithm Wrapper around GaussianBlur
class	MedianBlurFilter2DAlgorithm Wrapper around RankFilters
class	MedianBlurFilter3DAlgorithm Wrapper around GaussianBlur
class	MedianBlurGreyscale8U2DAlgorithm Wrapper around ImageProcessor
class	MedianBlurRGB2DAlgorithm Wrapper around ImageProcessor

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.blur with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
double	MedianBlurFilter2DAlgorithm.getRadius()
float	BoxFilter3DAlgorithm.getRadiusX()
float	MedianBlurFilter3DAlgorithm.getRadiusX()
float	BoxFilter3DAlgorithm.getRadiusY()
float	MedianBlurFilter3DAlgorithm.getRadiusY()
float	BoxFilter3DAlgorithm.getRadiusZ()
float	MedianBlurFilter3DAlgorithm.getRadiusZ()
double	GaussianBlur2DAlgorithm.getSigmaX()
double	GaussianBlur3DAlgorithm.getSigmaX()
double	GaussianBlur2DAlgorithm.getSigmaY()
double	GaussianBlur3DAlgorithm.getSigmaY()
double	GaussianBlur3DAlgorithm.getSigmaZ()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.calibration

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.calibration with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DrawScaleBarAlgorithm
class	SetPhysicalDimensionsAlgorithm
class	SetPhysicalDimensionsByAnnotationsAlgorithm
class	SetPhysicalDimensionsByExpressionsAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.calibration with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalColorParameter	DrawScaleBarAlgorithm.getBackgroundColor()
Color	DrawScaleBarAlgorithm.getBarColor()
int	DrawScaleBarAlgorithm.getBarThickness()
FontFamilyParameter	DrawScaleBarAlgorithm.TextSettings.getFontFamily()
int	DrawScaleBarAlgorithm.TextSettings.getFontSize()
FontStyleParameter	DrawScaleBarAlgorithm.TextSettings.getFontStyle()
OptionalQuantity	DrawScaleBarAlgorithm.getHorizontalBarSize()
DefaultExpressionParameter	DrawScaleBarAlgorithm.TextSettings.getHorizontalLabel()
ScaleBarGenerator.ScaleBarPosition	DrawScaleBarAlgorithm.getLocation()
OptionalDefaultExpressionParameter	SetPhysicalDimensionsByExpressionsAlgorithm.getPhysicalDimensionT()
OptionalQuantity	SetPhysicalDimensionsAlgorithm.getPhysicalDimensionT()
OptionalAnnotationNameParameter	SetPhysicalDimensionsByAnnotationsAlgorithm.getPhysicalDimensionT()
OptionalDefaultExpressionParameter	SetPhysicalDimensionsByExpressionsAlgorithm.getPhysicalDimensionValue()
OptionalQuantity	SetPhysicalDimensionsAlgorithm.getPhysicalDimensionValue()
OptionalAnnotationNameParameter	SetPhysicalDimensionsByAnnotationsAlgorithm.getPhysicalDimensionValue()
OptionalDefaultExpressionParameter	SetPhysicalDimensionsByExpressionsAlgorithm.getPhysicalDimensionX()
OptionalQuantity	SetPhysicalDimensionsAlgorithm.getPhysicalDimensionX()
OptionalAnnotationNameParameter	SetPhysicalDimensionsByAnnotationsAlgorithm.getPhysicalDimensionX()
OptionalDefaultExpressionParameter	SetPhysicalDimensionsByExpressionsAlgorithm.getPhysicalDimensionY()
OptionalQuantity	SetPhysicalDimensionsAlgorithm.getPhysicalDimensionY()
OptionalAnnotationNameParameter	SetPhysicalDimensionsByAnnotationsAlgorithm.getPhysicalDimensionY()
OptionalDefaultExpressionParameter	SetPhysicalDimensionsByExpressionsAlgorithm.getPhysicalDimensionZ()
OptionalQuantity	SetPhysicalDimensionsAlgorithm.getPhysicalDimensionZ()
OptionalAnnotationNameParameter	SetPhysicalDimensionsByAnnotationsAlgorithm.getPhysicalDimensionZ()
Color	DrawScaleBarAlgorithm.TextSettings.getTextColor()
DrawScaleBarAlgorithm.TextSettings	DrawScaleBarAlgorithm.getTextSettings()
OptionalQuantity	DrawScaleBarAlgorithm.getVerticalBarSize()
DefaultExpressionParameter	DrawScaleBarAlgorithm.TextSettings.getVerticalLabel()
boolean	DrawScaleBarAlgorithm.isDrawHorizontal()
boolean	DrawScaleBarAlgorithm.isDrawVertical()
boolean	DrawScaleBarAlgorithm.TextSettings.isHideLabels()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.colocalization

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.colocalization with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	Coloc2Node

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.colocalization with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	Coloc2Node.getChannel1Name()
String	Coloc2Node.getChannel2Name()
int	Coloc2Node.Settings.getCostesRandomizations()
OptionalAnnotationNameParameter	Coloc2Node.getHistogramNameAnnotation()
OptionalAnnotationNameParameter	Coloc2Node.getPlotNameAnnotation()
int	Coloc2Node.Settings.getPsf()
Coloc2Node.Settings	Coloc2Node.getSettings()
AutoThresholdRegression.Implementation	Coloc2Node.Settings.getThresholdRegression()
boolean	Coloc2Node.Settings.isCostesSignificanceTest()
boolean	Coloc2Node.isInputMasks()
boolean	Coloc2Node.Settings.isIntensityHistogram2D()
boolean	Coloc2Node.Settings.isKendallTauRankCorrelation()
boolean	Coloc2Node.Settings.isLiHistogramChannel1()
boolean	Coloc2Node.Settings.isLiHistogramChannel2()
boolean	Coloc2Node.Settings.isLiICQ()
boolean	Coloc2Node.Settings.isMandersCorrelation()
boolean	Coloc2Node.isOutputWarnings()
boolean	Coloc2Node.Settings.isSpearmanRankCorrelation()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.color

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ArrangeChannelsAlgorithm Wrapper around ChannelArranger
class	BlendImagesAlgorithm
class	ColorToGreyscaleExpression2D
class	CombineChannelsToRGBAlgorithm
class	InvertColorsAlgorithm Wrapper around ImageProcessor
class	MergeChannelsAlgorithm Wrapper around ImageProcessor
class	NewSplitChannelsAlgorithm Wrapper around ChannelSplitter
class	OverlayImagesAlgorithm Deprecated. Use BlendImagesAlgorithm instead
class	RenderImageToRGBAlgorithm
class	SetToColorAlgorithm
class	SetToValueAlgorithm
class	SplitChannelsAlgorithm Deprecated.
class	SplitRGBChannelsAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.color with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	SplitChannelsAlgorithm.getAnnotationColumnChannelIndex() Deprecated.
String	SplitChannelsAlgorithm.getAnnotationColumnSlotName() Deprecated.
BlendImagesAlgorithm.BlendMode	BlendImagesAlgorithm.Layer.getBlendMode()
InputSlotMapParameterCollection	OverlayImagesAlgorithm.getChannelColorAssignment() Deprecated.
InputSlotMapParameterCollection	MergeChannelsAlgorithm.getChannelColorAssignment()
OptionalAnnotationNameParameter	NewSplitChannelsAlgorithm.getChannelIndexAnnotation()
OptionalAnnotationNameParameter	NewSplitChannelsAlgorithm.getChannelNameAnnotation()
IntegerAndIntegerPairParameter.List	ArrangeChannelsAlgorithm.getChannelReordering()
OutputSlotMapParameterCollection	SplitChannelsAlgorithm.getChannelToSlotAssignment() Deprecated.
OutputSlotMapParameterCollection	NewSplitChannelsAlgorithm.getChannelToSlotAssignment()
Color	OverlayImagesAlgorithm.Channel.getColor()
Color	SetToColorAlgorithm.getColor()
DefaultExpressionParameter	ColorToGreyscaleExpression2D.getExpression()
InputSlotMapParameterCollection	BlendImagesAlgorithm.getLayers()
double	OverlayImagesAlgorithm.Channel.getOpacity()
double	BlendImagesAlgorithm.Layer.getOpacity()
JIPipeDataInfoRef	ColorToGreyscaleExpression2D.getOutputType()
int	BlendImagesAlgorithm.Layer.getPriority()
double	SetToValueAlgorithm.getValue()
boolean	SplitChannelsAlgorithm.isAnnotateWithChannelIndex() Deprecated.
boolean	SplitChannelsAlgorithm.isAnnotateWithSlotName() Deprecated.
boolean	OverlayImagesAlgorithm.Channel.isBlackToAlpha()
boolean	MergeChannelsAlgorithm.isCreateComposite()
boolean	SplitChannelsAlgorithm.isIgnoreMissingChannels() Deprecated.
boolean	NewSplitChannelsAlgorithm.isIgnoreMissingChannels()
boolean	ArrangeChannelsAlgorithm.isKeepSameChannelCount()
boolean	BlendImagesAlgorithm.isRenderGreyscaleImages()
void	ArrangeChannelsAlgorithm.setToExample(JIPipeWorkbench parent)

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.contrast

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.contrast with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CLAHEContrastEnhancer Applies CLAHE image enhancing
class	HistogramContrastEnhancerAlgorithm This class is based on ContrastEnhancer This class is not very portable, so I adapted the code here
class	IlluminationCorrection2DAlgorithm Applies illumination correction

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.contrast with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	CLAHEContrastEnhancer.getBins()
int	CLAHEContrastEnhancer.getBlockRadius()
GaussianBlur2DAlgorithm	IlluminationCorrection2DAlgorithm.getGaussianAlgorithm()
float	CLAHEContrastEnhancer.getMaxSlope()
HistogramContrastEnhancerAlgorithm.Method	HistogramContrastEnhancerAlgorithm.getMethod()
double	HistogramContrastEnhancerAlgorithm.getSaturatedPixels()
boolean	CLAHEContrastEnhancer.isFastMode()
boolean	HistogramContrastEnhancerAlgorithm.isUseStackHistogram()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.convert

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.convert with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ConvertImageAlgorithm
class	ConvertImageTo16BitAlgorithm
class	ConvertImageTo32BitAlgorithm
class	ConvertImageTo8BitAlgorithm
class	ConvertImageToHSBAlgorithm
class	ConvertImageToLABAlgorithm
class	ImageToMatrixAlgorithm Algorithm that generates ResultsTableData as histogram
class	ImageToTableAlgorithm Algorithm that generates ResultsTableData as histogram
class	MatrixToImageAlgorithm
class	TableToImageAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.convert with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeDynamicParameterCollection	TableToImageAlgorithm.getColumnAssignment()
OptionalIntegerParameter	TableToImageAlgorithm.getCustomHeight()
OptionalIntegerParameter	TableToImageAlgorithm.getCustomSizeC()
OptionalIntegerParameter	TableToImageAlgorithm.getCustomSizeT()
OptionalIntegerParameter	TableToImageAlgorithm.getCustomSizeZ()
OptionalIntegerParameter	TableToImageAlgorithm.getCustomWidth()
JIPipeDataInfoRef	ConvertImageAlgorithm.getGeneratedImageType()
JIPipeDataInfoRef	MatrixToImageAlgorithm.getOutputImageType()
JIPipeDataInfoRef	TableToImageAlgorithm.getOutputImageType()
String	ImageToTableAlgorithm.getSliceAnnotation()
boolean	ImageToTableAlgorithm.isApplyPerSlice()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.convolve

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.convolve with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ConvolveByImage2DAlgorithm Wrapper around Convolver
class	ConvolveByParameter2DAlgorithm Wrapper around Convolver

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.convolve with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Matrix2DFloat	ConvolveByParameter2DAlgorithm.getMatrix()
boolean	ConvolveByParameter2DAlgorithm.isNormalize()
boolean	ConvolveByImage2DAlgorithm.isNormalize()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.datasources

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImageStackFromFolder Loads an image data from a file via IJ.openFile()
class	OMEImageFromImagePlus

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OMEExporterSettings	OMEImageFromImagePlus.getExporterSettings()
PathQueryExpression	ImageStackFromFolder.getFilterExpression()
JIPipeDataInfoRef	ImageStackFromFolder.getGeneratedImageType()
HyperstackDimension	ImageStackFromFolder.getOutputDimension()
IntegerRange	ImageStackFromFolder.getSlicesToImport()
boolean	ImageStackFromFolder.isIgnoreInvalidSlices()
boolean	ImageStackFromFolder.isRemoveLut()
boolean	ImageStackFromFolder.isSortFilesNumerically()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.dimensions

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.dimensions with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CreateStackAlgorithm Wrapper around ImageProcessor
class	ExpressionSlicerAlgorithm
class	HyperstackSlicerAlgorithm
class	InputImagesToMontage
class	Merge2DToHyperstackAlgorithm
class	MontageToStackAlgorithm Implementation of MontageMaker
class	NewZProjectorAlgorithm Wrapper around ZProjector
class	ReorderDimensionsAlgorithm Algorithm that reorders Hyperstack dimensions
class	ResliceAlgorithm
class	SplitByDimensionAlgorithm
class	StackCombinerAlgorithm
class	StackInverterAlgorithm Wrapper around ImageProcessor
class	StackSplitterAlgorithm Wrapper around ChannelArranger
class	StackTo2DAlgorithm Wrapper around ImageProcessor
class	StackToDimensionMergerAlgorithm Wrapper around ImageProcessor
class	StackToMontageAlgorithm Implementation of MontageMaker
class	ZProjectorAlgorithm Wrapper around ZProjector

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.dimensions with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalAnnotationNameParameter	HyperstackSlicerAlgorithm.getAnnotateC()
OptionalAnnotationNameParameter	ExpressionSlicerAlgorithm.getAnnotateC()
OptionalAnnotationNameParameter	HyperstackSlicerAlgorithm.getAnnotateT()
OptionalAnnotationNameParameter	ExpressionSlicerAlgorithm.getAnnotateT()
OptionalAnnotationNameParameter	HyperstackSlicerAlgorithm.getAnnotateZ()
OptionalAnnotationNameParameter	ExpressionSlicerAlgorithm.getAnnotateZ()
OptionalAnnotationNameParameter	StackTo2DAlgorithm.getAnnotationC()
OptionalAnnotationNameParameter	StackTo2DAlgorithm.getAnnotationIndex()
JIPipeTextAnnotationMergeMode	SplitByDimensionAlgorithm.getAnnotationMergeStrategy()
OptionalAnnotationNameParameter	StackTo2DAlgorithm.getAnnotationT()
String	StackSplitterAlgorithm.getAnnotationType()
OptionalAnnotationNameParameter	StackTo2DAlgorithm.getAnnotationZ()
Color	InputImagesToMontage.getBackgroundColor()
Color	StackToMontageAlgorithm.getBackgroundColor()
int	MontageToStackAlgorithm.getBorderWidth()
int	InputImagesToMontage.getBorderWidth()
int	StackToMontageAlgorithm.getBorderWidth()
CanvasEqualizer	InputImagesToMontage.getCanvasEqualizer()
int	MontageToStackAlgorithm.getColumns()
OptionalIntegerParameter	InputImagesToMontage.getColumns()
OptionalIntegerParameter	StackToMontageAlgorithm.getColumns()
String	CreateStackAlgorithm.getCounterAnnotation()
HyperstackDimension	StackToDimensionMergerAlgorithm.getCreatedDimension()
DefaultExpressionParameter	ExpressionSlicerAlgorithm.getExpressionC()
DefaultExpressionParameter	ExpressionSlicerAlgorithm.getExpressionT()
DefaultExpressionParameter	ExpressionSlicerAlgorithm.getExpressionZ()
OptionalIntegerParameter	StackToMontageAlgorithm.getFirstIndex()
int	InputImagesToMontage.getFontSize()
int	StackToMontageAlgorithm.getFontSize()
Color	InputImagesToMontage.getForegroundColor()
Color	StackToMontageAlgorithm.getForegroundColor()
int	StackToMontageAlgorithm.getIndexIncrement()
IntegerRange	HyperstackSlicerAlgorithm.getIndicesC()
IntegerRange	HyperstackSlicerAlgorithm.getIndicesT()
IntegerRange	HyperstackSlicerAlgorithm.getIndicesZ()
JIPipeDataByMetadataExporter	InputImagesToMontage.getLabelGenerator()
OptionalIntegerParameter	StackToMontageAlgorithm.getLastIndex()
ZProjectorAlgorithm.Method	ZProjectorAlgorithm.getMethod()
ZProjectorAlgorithm.Method	NewZProjectorAlgorithm.getMethod()
HyperstackDimension	CreateStackAlgorithm.getOutputDimension()
OutputSlotMapParameterCollection	SplitByDimensionAlgorithm.getOutputIndices()
Anchor	ResliceAlgorithm.getPlaneStartLocation()
HyperstackDimension	NewZProjectorAlgorithm.getProjectedAxis()
OptionalIntegerRange	NewZProjectorAlgorithm.getRestrictToIndices()
int	MontageToStackAlgorithm.getRows()
OptionalIntegerParameter	InputImagesToMontage.getRows()
OptionalIntegerParameter	StackToMontageAlgorithm.getRows()
double	InputImagesToMontage.getScale()
double	StackToMontageAlgorithm.getScale()
DefaultExpressionParameter	Merge2DToHyperstackAlgorithm.getSliceCLocation()
DefaultExpressionParameter	Merge2DToHyperstackAlgorithm.getSliceTLocation()
DefaultExpressionParameter	Merge2DToHyperstackAlgorithm.getSliceZLocation()
OutputSlotMapParameterCollection	StackSplitterAlgorithm.getStackAssignments()
int	ZProjectorAlgorithm.getStartSlice()
int	ZProjectorAlgorithm.getStopSlice()
HyperstackDimension	ReorderDimensionsAlgorithm.getTargetC()
HyperstackDimension	StackCombinerAlgorithm.getTargetDimension()
HyperstackDimension	SplitByDimensionAlgorithm.getTargetDimension()
OptionalAnnotationNameParameter	SplitByDimensionAlgorithm.getTargetDimensionAnnotation()
HyperstackDimension	ReorderDimensionsAlgorithm.getTargetT()
HyperstackDimension	ReorderDimensionsAlgorithm.getTargetZ()
boolean	InputImagesToMontage.isDrawLabels()
boolean	ResliceAlgorithm.isFlipVertical()
boolean	StackSplitterAlgorithm.isIgnoreMissingSlices()
boolean	ExpressionSlicerAlgorithm.isIteratePerC()
boolean	ExpressionSlicerAlgorithm.isIteratePerT()
boolean	ExpressionSlicerAlgorithm.isIteratePerZ()
boolean	StackToMontageAlgorithm.isLabels()
boolean	ResliceAlgorithm.isNoInterpolation()
boolean	ZProjectorAlgorithm.isProjectAllHyperstackTimePoints()
boolean	ExpressionSlicerAlgorithm.isRemoveDuplicates()
boolean	ResliceAlgorithm.isRotate()
boolean	StackSplitterAlgorithm.isSortedStackIds()
boolean	StackSplitterAlgorithm.isUniqueStackIds()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.edge

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.edge with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CannyEdgeDetectorAlgorithm This is the JIPipe version of the ImageJ plugin ...
class	LaplacianEdgeDetectorAlgorithm Wrapper around ImageProcessor
class	SobelEdgeDetectorAlgorithm Wrapper around ImageProcessor

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.edge with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
float	CannyEdgeDetectorAlgorithm.getGaussianKernelRadius()
int	CannyEdgeDetectorAlgorithm.getGaussianKernelWidth()
double	CannyEdgeDetectorAlgorithm.getHighThreshold()
double	CannyEdgeDetectorAlgorithm.getLowThreshold()
LaplacianEdgeDetectorAlgorithm.Mode	LaplacianEdgeDetectorAlgorithm.getMode()
boolean	CannyEdgeDetectorAlgorithm.isNormalizeContrast()
boolean	LaplacianEdgeDetectorAlgorithm.isRemoveNegativeValues()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.features

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.features with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DifferenceOfGaussian2DAlgorithm Wrapper around GaussianBlur
class	DirectionalFilter2DAlgorithm
class	FrangiVesselnessFeatures Applies CLAHE image enhancing
class	LaplacianOfGaussian2DAlgorithm Based on code by Dimiter Prodanov ...
class	LocalMaxima2DAlgorithm Wrapper around MaximumFinder
class	MeijeringVesselness2DFeatures Applies CLAHE image enhancing

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.features with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
double	MeijeringVesselness2DFeatures.getAlpha()
double	LocalMaxima2DAlgorithm.getHeightTolerance()
int	DirectionalFilter2DAlgorithm.getLineLength()
double	FrangiVesselnessFeatures.getMaximumScale()
double	FrangiVesselnessFeatures.getMinimumScale()
int	DirectionalFilter2DAlgorithm.getnDirections()
int	FrangiVesselnessFeatures.getNumScales()
inra.ijpb.morphology.directional.DirectionalFilter.Operation	DirectionalFilter2DAlgorithm.getOperation()
LocalMaxima2DAlgorithm.OutputType	LocalMaxima2DAlgorithm.getOutputType()
int	LaplacianOfGaussian2DAlgorithm.getRadius()
DoubleList	MeijeringVesselness2DFeatures.getScales()
double	DifferenceOfGaussian2DAlgorithm.getSigma0X()
double	DifferenceOfGaussian2DAlgorithm.getSigma0Y()
double	DifferenceOfGaussian2DAlgorithm.getSigma1X()
double	DifferenceOfGaussian2DAlgorithm.getSigma1Y()
FrangiVesselnessFeatures.SlicingMode	FrangiVesselnessFeatures.getSlicingMode()
double	LocalMaxima2DAlgorithm.getThreshold()
inra.ijpb.morphology.directional.DirectionalFilter.Type	DirectionalFilter2DAlgorithm.getType()
boolean	LocalMaxima2DAlgorithm.isExcludeOnEdges()
boolean	LocalMaxima2DAlgorithm.isInputIsEDM()
boolean	FrangiVesselnessFeatures.isInvert()
boolean	MeijeringVesselness2DFeatures.isInvert()
boolean	LocalMaxima2DAlgorithm.isStrict()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.fft

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.fft with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	FFT2DForwardTransform Applies a FFT forward transformation
class	FFT2DInverseTransform Applies a FFT forward transformation
class	FFT2DSwapQuadrants Applies a FFT forward transformation

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.forms

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.forms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DrawMaskAlgorithm
class	DrawROIAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.forms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalIntegerParameter	DrawROIAlgorithm.getOverwriteSizeC()
OptionalIntegerParameter	DrawMaskAlgorithm.getOverwriteSizeC()
OptionalIntegerParameter	DrawROIAlgorithm.getOverwriteSizeT()
OptionalIntegerParameter	DrawMaskAlgorithm.getOverwriteSizeT()
OptionalIntegerParameter	DrawROIAlgorithm.getOverwriteSizeZ()
OptionalIntegerParameter	DrawMaskAlgorithm.getOverwriteSizeZ()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.generate

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.generate with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	GenerateLUTImageFromColorMap Wrapper around ImageProcessor
class	GenerateMissingImageFromMathExpression2D Wrapper around ImageProcessor
class	GenerateMissingTablesAlgorithm
class	GenerateMissingZeroImage Wrapper around ImageProcessor
class	GenerateStructureElement2DAlgorithm Wrapper around ImageProcessor
class	GenerateStructureElement3DAlgorithm Wrapper around ImageProcessor
class	GenerateZeroImage Wrapper around ImageProcessor
class	ImageFromMatrix2DAlgorithm Wrapper around Convolver

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.generate with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ColorMap	GenerateLUTImageFromColorMap.getColorMap()
JIPipeDataInfoRef	GenerateZeroImage.getDataType()
inra.ijpb.morphology.Strel3D.Shape	GenerateStructureElement3DAlgorithm.getElement()
inra.ijpb.morphology.Strel.Shape	GenerateStructureElement2DAlgorithm.getElement()
DefaultExpressionParameter	GenerateMissingImageFromMathExpression2D.getFunction()
int	GenerateZeroImage.getHeight()
int	GenerateLUTImageFromColorMap.getHeight()
Matrix2DFloat	ImageFromMatrix2DAlgorithm.getMatrix()
OptionalIntegerParameter	GenerateMissingImageFromMathExpression2D.getOverwriteHeight()
OptionalIntegerParameter	GenerateMissingZeroImage.getOverwriteHeight()
OptionalBitDepth	GenerateMissingImageFromMathExpression2D.getOverwriteOutputBitDepth()
OptionalBitDepth	GenerateMissingZeroImage.getOverwriteOutputBitDepth()
OptionalIntegerParameter	GenerateMissingImageFromMathExpression2D.getOverwriteSizeC()
OptionalIntegerParameter	GenerateMissingZeroImage.getOverwriteSizeC()
OptionalIntegerParameter	GenerateMissingImageFromMathExpression2D.getOverwriteSizeT()
OptionalIntegerParameter	GenerateMissingZeroImage.getOverwriteSizeT()
OptionalIntegerParameter	GenerateMissingImageFromMathExpression2D.getOverwriteSizeZ()
OptionalIntegerParameter	GenerateMissingZeroImage.getOverwriteSizeZ()
OptionalIntegerParameter	GenerateMissingImageFromMathExpression2D.getOverwriteWidth()
OptionalIntegerParameter	GenerateMissingZeroImage.getOverwriteWidth()
ResultsTableData	GenerateMissingTablesAlgorithm.getPlaceholderTable()
int	GenerateStructureElement3DAlgorithm.getRadius()
int	GenerateStructureElement2DAlgorithm.getRadius()
int	GenerateZeroImage.getSizeC()
int	GenerateZeroImage.getSizeT()
int	GenerateZeroImage.getSizeZ()
int	GenerateZeroImage.getWidth()
int	GenerateLUTImageFromColorMap.getWidth()
boolean	GenerateMissingImageFromMathExpression2D.isGenerateOnePerBatch()
boolean	GenerateMissingZeroImage.isGenerateOnePerBatch()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.io

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.io with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ExportImage2Algorithm
class	ExportImageAlgorithm
class	ExportROIAlgorithm
class	ExportTableAlgorithm
class	ExportTableAsXLSXAlgorithm
class	ImagePlusFromGUI Imports ImagePlusData from the GUI
class	ImagePlusToGUI Imports ImagePlusData from the GUI
class	ResultsTableFromGUI Imports ImagePlusData from the GUI
class	ResultsTableToGUI Imports ImagePlusData from the GUI
class	ROIFromGUI Imports ImagePlusData from the GUI
class	ROIToGUI Imports ImagePlusData from the GUI
class	RunImageJExporterAlgorithm
class	RunImageJImporterAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.io with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
AVICompression	ExportImageAlgorithm.getAviCompression()
AVICompression	ExportImage2Algorithm.getAviCompression()
JIPipeDataByMetadataExporter	ExportImageAlgorithm.getExporter()
JIPipeDataByMetadataExporter	ExportROIAlgorithm.getExporter()
JIPipeDataByMetadataExporter	ExportImage2Algorithm.getExporter()
JIPipeDataByMetadataExporter	ExportTableAlgorithm.getExporter()
JIPipeDataByMetadataExporter	ExportTableAsXLSXAlgorithm.getExporter()
ImageJDataExporterRef	RunImageJExporterAlgorithm.getExporterType()
ImageJExportParameters	RunImageJExporterAlgorithm.getExportParameters()
ExportImageAlgorithm.FileFormat	ExportImageAlgorithm.getFileFormat()
ExportImageAlgorithm.FileFormat	ExportImage2Algorithm.getFileFormat()
ExportTableAlgorithm.FileFormat	ExportTableAlgorithm.getFileFormat()
DefaultExpressionParameter	ImagePlusFromGUI.getImageFilters()
LogicalOperation	ImagePlusFromGUI.getImageFiltersOperation()
ImageJDataImporterRef	RunImageJImporterAlgorithm.getImporterType()
ImageJImportParameters	RunImageJImporterAlgorithm.getImportParameters()
int	ExportImageAlgorithm.getJpegQuality()
int	ExportImage2Algorithm.getJpegQuality()
HyperstackDimension	ExportImageAlgorithm.getMovieAnimatedDimension()
HyperstackDimension	ExportImage2Algorithm.getMovieAnimatedDimension()
int	ExportImageAlgorithm.getMovieFrameTime()
int	ExportImage2Algorithm.getMovieFrameTime()
DefaultExpressionParameter	ExportTableAsXLSXAlgorithm.getOrderExpression()
Path	ExportImageAlgorithm.getOutputDirectory()
Path	ExportROIAlgorithm.getOutputDirectory()
Path	ExportTableAlgorithm.getOutputDirectory()
Path	ExportTableAsXLSXAlgorithm.getOutputDirectory()
DefaultExpressionParameter	ResultsTableFromGUI.getTitleFilterExpression()
boolean	ExportROIAlgorithm.isExportAsROIFile()
boolean	ImagePlusFromGUI.isOnlyActiveImage()
boolean	ExportImageAlgorithm.isRelativeToProjectDir()
boolean	ExportROIAlgorithm.isRelativeToProjectDir()
boolean	ExportTableAlgorithm.isRelativeToProjectDir()
boolean	ExportTableAsXLSXAlgorithm.isRelativeToProjectDir()
void	RunImageJExporterAlgorithm.setExporterParametersFromUI(JIPipeWorkbench parent)
void	RunImageJImporterAlgorithm.setImporterParametersFromUI(JIPipeWorkbench parent)
void	ExportTableAsXLSXAlgorithm.setOrderExpression(DefaultExpressionParameter orderExpression)

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AnnotateWithOverlapMeasureLabelsAlgorithm
class	CropLabelsAlgorithm
class	DilateLabelsAlgorithm
class	ExpandLabelsAlgorithm
class	ExtractLabelStatisticsAlgorithm
class	GetLabelBoundariesAlgorithm
class	KeepLargestLabelAlgorithm
class	LabelsToRGBAlgorithm
class	LabelsToROIAlgorithm
class	MergeLabelsAlgorithm
class	MergeSmallLabelsAlgorithm
class	OverlapMeasureLabelsAlgorithm
class	RemapLabelsAlgorithm
class	ReplaceLabelsAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Color	LabelsToRGBAlgorithm.getBackgroundColor()
int	CropLabelsAlgorithm.getBorder()
inra.ijpb.color.ColorMaps.CommonLabelMaps	LabelsToRGBAlgorithm.getColorMap()
Neighborhood2D	LabelsToROIAlgorithm.getConnectivity()
OptionalAnnotationNameParameter	AnnotateWithOverlapMeasureLabelsAlgorithm.getDiceCoefficientAnnotation()
OptionalAnnotationNameParameter	AnnotateWithOverlapMeasureLabelsAlgorithm.getFalseNegativeErrorAnnotation()
OptionalAnnotationNameParameter	AnnotateWithOverlapMeasureLabelsAlgorithm.getFalsePositiveErrorAnnotation()
OptionalAnnotationNameParameter	AnnotateWithOverlapMeasureLabelsAlgorithm.getJaccardIndexAnnotation()
OptionalAnnotationNameParameter	CropLabelsAlgorithm.getLabelIdAnnotation()
OptionalIntegerRange	CropLabelsAlgorithm.getLabelIdLimit()
DefaultExpressionParameter	LabelsToROIAlgorithm.getLabelNameExpression()
double	DilateLabelsAlgorithm.getMaxRadius()
OverlapStatisticsSetParameter	OverlapMeasureLabelsAlgorithm.getMeasurements()
ImageStatisticsSetParameter	ExtractLabelStatisticsAlgorithm.getMeasurements()
LabelsToROIAlgorithm.Method	LabelsToROIAlgorithm.getMethod()
int	MergeSmallLabelsAlgorithm.getMinimumNumberOfPixels()
float	ExpandLabelsAlgorithm.getRatio()
IntRangeAndIntegerPairParameter.List	ReplaceLabelsAlgorithm.getReplacements()
ImageROITargetArea	MergeSmallLabelsAlgorithm.getSourceArea()
OptionalAnnotationNameParameter	AnnotateWithOverlapMeasureLabelsAlgorithm.getTotalOverlapAnnotation()
OptionalAnnotationNameParameter	AnnotateWithOverlapMeasureLabelsAlgorithm.getVolumeSimilarityAnnotation()
boolean	MergeSmallLabelsAlgorithm.isExcludeZero()
boolean	ExtractLabelStatisticsAlgorithm.isMeasureInPhysicalUnits()
boolean	MergeSmallLabelsAlgorithm.isMergeToLargerLabel()
boolean	LabelsToRGBAlgorithm.isShuffleLut()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels.filter

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels.filter with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	FilterLabelsByExpression2DAlgorithm
class	FilterLabelsByExpression3DAlgorithm
class	FilterLabelsByIdAlgorithm
class	FilterLabelsByMaskAlgorithm
class	FilterLabelsByOverlapAlgorithm
class	FilterLabelsByStatisticsAlgorithm Wrapper around RoiManager
class	RemoveBorderLabelsAlgorithm
class	RemoveLargestLabelAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels.filter with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
CustomExpressionVariablesParameter	FilterLabelsByStatisticsAlgorithm.getCustomFilterVariables()
CustomExpressionVariablesParameter	FilterLabelsByOverlapAlgorithm.getCustomVariables()
DefaultExpressionParameter	FilterLabelsByExpression2DAlgorithm.getExpression()
DefaultExpressionParameter	FilterLabelsByExpression3DAlgorithm.getExpression()
DefaultExpressionParameter	FilterLabelsByStatisticsAlgorithm.getFilters()
int	RemoveLargestLabelAlgorithm.getIterations()
FilterLabelsByOverlapAlgorithm.LabelFilterSettings	FilterLabelsByOverlapAlgorithm.getLabels1Settings()
FilterLabelsByOverlapAlgorithm.LabelFilterSettings	FilterLabelsByOverlapAlgorithm.getLabels2Settings()
ImageStatisticsSetParameter	FilterLabelsByStatisticsAlgorithm.getMeasurements()
DefaultExpressionParameter	FilterLabelsByOverlapAlgorithm.LabelFilterSettings.getOverlapFilter()
ImageStatisticsSetParameter	FilterLabelsByOverlapAlgorithm.getOverlapFilterMeasurements()
IntegerRange	FilterLabelsByIdAlgorithm.getValues()
boolean	FilterLabelsByMaskAlgorithm.isDeleteMaskedLabels()
boolean	FilterLabelsByOverlapAlgorithm.LabelFilterSettings.isEnabled()
boolean	FilterLabelsByOverlapAlgorithm.LabelFilterSettings.isInvert()
boolean	FilterLabelsByIdAlgorithm.isKeepValues()
boolean	FilterLabelsByStatisticsAlgorithm.isMeasureInPhysicalUnits()
boolean	FilterLabelsByOverlapAlgorithm.LabelFilterSettings.isMeasureInPhysicalUnits()
boolean	FilterLabelsByOverlapAlgorithm.LabelFilterSettings.isOutputOverlaps()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.lut

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.lut with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ApplyLUTAlgorithm
class	LUTInverterAlgorithm
class	RemoveLUTAlgorithm
class	SetLUTFromColorMapAlgorithm
class	SetLUTFromColorsAlgorithm
class	SetLUTFromImageAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.lut with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ColorMap	SetLUTFromColorMapAlgorithm.getColorMap()
Color	SetLUTFromColorsAlgorithm.getFirstColor()
Color	SetLUTFromColorsAlgorithm.getSecondColor()
boolean	SetLUTFromColorMapAlgorithm.isApplyToAllPlanes()
boolean	RemoveLUTAlgorithm.isApplyToAllPlanes()
boolean	SetLUTFromColorsAlgorithm.isApplyToAllPlanes()
boolean	LUTInverterAlgorithm.isApplyToAllPlanes()
boolean	SetLUTFromImageAlgorithm.isApplyToAllPlanes()
boolean	SetLUTFromColorMapAlgorithm.isDuplicateImage()
boolean	RemoveLUTAlgorithm.isDuplicateImage()
boolean	SetLUTFromColorsAlgorithm.isDuplicateImage()
boolean	LUTInverterAlgorithm.isDuplicateImage()
boolean	SetLUTFromImageAlgorithm.isDuplicateImage()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ApplyColorMathExpression2DExpression
class	ApplyMath2DAlgorithm Wrapper around ImageProcessor
class	ApplyMathExpression2DAlgorithm Wrapper around ImageProcessor
class	ApplyTransform2DAlgorithm Wrapper around ImageProcessor
class	ApplyVectorMathExpression2DAlgorithm Wrapper around ImageProcessor
class	DivideByMaximumAlgorithm Wrapper around ImageProcessor
class	GenerateFromMathExpression2D Wrapper around ImageProcessor
class	GenerateVectorFromMathExpression Wrapper around ImageProcessor
class	Hessian2DAlgorithm Wrapper around EDM
class	ImageCalculator2DAlgorithm Wrapper around ImageProcessor
class	ImageCalculator2DExpression
class	RemoveNaNFilter2DAlgorithm Wrapper around RankFilters
class	RoundFloatImageAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
HyperstackDimension	ApplyVectorMathExpression2DAlgorithm.getComponentDimension()
HyperstackDimension	GenerateVectorFromMathExpression.getComponentDimension()
int	RoundFloatImageAlgorithm.getDecimals()
EigenvalueSelection2D	Hessian2DAlgorithm.getEigenvalueSelection2D()
DefaultExpressionParameter	ImageCalculator2DExpression.getExpression()
DefaultExpressionParameter	ApplyColorMathExpression2DExpression.getExpression()
DefaultExpressionParameter	GenerateFromMathExpression2D.getFunction()
DefaultExpressionParameter	GenerateVectorFromMathExpression.getFunction()
int	GenerateFromMathExpression2D.getHeight()
int	GenerateVectorFromMathExpression.getHeight()
InputSlotMapParameterCollection	ImageCalculator2DAlgorithm.getOperands()
ImageCalculator2DAlgorithm.Operation	ImageCalculator2DAlgorithm.getOperation()
JIPipeDataInfoRef	ApplyColorMathExpression2DExpression.getOutputType()
int	ApplyVectorMathExpression2DAlgorithm.getOutputVectorSize()
double	RemoveNaNFilter2DAlgorithm.getRadius()
int	GenerateFromMathExpression2D.getSizeC()
int	GenerateVectorFromMathExpression.getSizeC()
int	GenerateFromMathExpression2D.getSizeT()
int	GenerateVectorFromMathExpression.getSizeT()
int	GenerateFromMathExpression2D.getSizeZ()
int	GenerateVectorFromMathExpression.getSizeZ()
double	Hessian2DAlgorithm.getSmoothing()
ApplyTransform2DAlgorithm.Transformation	ApplyTransform2DAlgorithm.getTransformation()
DefaultExpressionParameter	ApplyVectorMathExpression2DAlgorithm.getTransformation()
ApplyMath2DAlgorithm.Transformation	ApplyMath2DAlgorithm.getTransformation()
DefaultExpressionParameter	ApplyMathExpression2DAlgorithm.getTransformation()
double	ApplyMath2DAlgorithm.getValue()
int	GenerateFromMathExpression2D.getWidth()
int	GenerateVectorFromMathExpression.getWidth()
boolean	Hessian2DAlgorithm.isCompareAbsolute()
boolean	ImageCalculator2DAlgorithm.isFloatingPointOutput()
boolean	DivideByMaximumAlgorithm.isRecalibrate()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math.distancemap

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math.distancemap with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ApplyDistanceTransform2DAlgorithm Wrapper around EDM
class	ChamferDistanceMap2DAlgorithm
class	ChamferDistanceMap3DAlgorithm
class	GeodesicDistanceMap2DAlgorithm
class	LabelChamferDistanceMap3DAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math.distancemap with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	ApplyDistanceTransform2DAlgorithm.getBackgroundValue()
inra.ijpb.binary.ChamferWeights3D	LabelChamferDistanceMap3DAlgorithm.getChamferWeights()
inra.ijpb.binary.ChamferWeights	ChamferDistanceMap2DAlgorithm.getChamferWeights()
inra.ijpb.binary.ChamferWeights3D	ChamferDistanceMap3DAlgorithm.getChamferWeights()
inra.ijpb.binary.ChamferWeights	GeodesicDistanceMap2DAlgorithm.getChamferWeights()
JIPipeDataInfoRef	LabelChamferDistanceMap3DAlgorithm.getOutputType()
JIPipeDataInfoRef	ChamferDistanceMap2DAlgorithm.getOutputType()
JIPipeDataInfoRef	ChamferDistanceMap3DAlgorithm.getOutputType()
JIPipeDataInfoRef	GeodesicDistanceMap2DAlgorithm.getOutputType()
boolean	ApplyDistanceTransform2DAlgorithm.isEdgesAreBackground()
boolean	LabelChamferDistanceMap3DAlgorithm.isNormalize()
boolean	ChamferDistanceMap2DAlgorithm.isNormalize()
boolean	ChamferDistanceMap3DAlgorithm.isNormalize()
boolean	GeodesicDistanceMap2DAlgorithm.isNormalize()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math.local

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math.local with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ExtendedMaxima2DAlgorithm
class	ExtendedMaxima3DAlgorithm
class	ExtendedMinima2DAlgorithm
class	ExtendedMinima3DAlgorithm
class	ImposeMaxima2DAlgorithm
class	ImposeMaxima3DAlgorithm
class	LocalImageCalculator2DExpression
class	LocalMaximumFilter2DAlgorithm Wrapper around RankFilters
class	LocalMaximumFilter3DAlgorithm Wrapper around RankFilters
class	LocalMinimumFilter2DAlgorithm Wrapper around RankFilters
class	LocalMinimumFilter3DAlgorithm Wrapper around RankFilters
class	LocalVarianceFilter2DAlgorithm Wrapper around RankFilters
class	LocalVarianceFilter3DAlgorithm Wrapper around RankFilters
class	RegionalMaxima2DAlgorithm
class	RegionalMaxima3DAlgorithm
class	RegionalMinima2DAlgorithm
class	RegionalMinima3DAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.math.local with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Neighborhood2D	ExtendedMinima2DAlgorithm.getConnectivity()
Neighborhood3D	ExtendedMinima3DAlgorithm.getConnectivity()
Neighborhood2D	RegionalMinima2DAlgorithm.getConnectivity()
Neighborhood3D	ExtendedMaxima3DAlgorithm.getConnectivity()
Neighborhood3D	RegionalMaxima3DAlgorithm.getConnectivity()
Neighborhood3D	RegionalMinima3DAlgorithm.getConnectivity()
Neighborhood2D	RegionalMaxima2DAlgorithm.getConnectivity()
Neighborhood2D	ExtendedMaxima2DAlgorithm.getConnectivity()
double	ExtendedMinima2DAlgorithm.getDynamic()
double	ExtendedMinima3DAlgorithm.getDynamic()
double	ExtendedMaxima3DAlgorithm.getDynamic()
double	ExtendedMaxima2DAlgorithm.getDynamic()
DefaultExpressionParameter	LocalImageCalculator2DExpression.getExpression()
int	LocalImageCalculator2DExpression.getLocalWindowHeight()
int	LocalImageCalculator2DExpression.getLocalWindowWidth()
double	LocalMinimumFilter2DAlgorithm.getRadius()
double	LocalVarianceFilter2DAlgorithm.getRadius()
double	LocalMaximumFilter2DAlgorithm.getRadius()
float	LocalMinimumFilter3DAlgorithm.getRadiusX()
float	LocalVarianceFilter3DAlgorithm.getRadiusX()
float	LocalMaximumFilter3DAlgorithm.getRadiusX()
float	LocalMinimumFilter3DAlgorithm.getRadiusY()
float	LocalVarianceFilter3DAlgorithm.getRadiusY()
float	LocalMaximumFilter3DAlgorithm.getRadiusY()
float	LocalMinimumFilter3DAlgorithm.getRadiusZ()
float	LocalVarianceFilter3DAlgorithm.getRadiusZ()
float	LocalMaximumFilter3DAlgorithm.getRadiusZ()
SourceWrapMode	LocalImageCalculator2DExpression.getSourceWrapMode()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.misc

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.misc with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DataToPreviewAlgorithm
class	RenderJIPipeProjectAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.misc with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	DataToPreviewAlgorithm.getPreviewHeight()
int	DataToPreviewAlgorithm.getPreviewWidth()
RenderPipelineRunSettings	RenderJIPipeProjectAlgorithm.getSettings()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.morphology

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.morphology with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	FindHoles2DAlgorithm
class	GrayscaleAttributeFiltering2DAlgorithm
class	GrayscaleAttributeFiltering3DAlgorithm
class	MorphologicalReconstruction2DAlgorithm
class	MorphologicalReconstruction3DAlgorithm
class	Morphology2DAlgorithm Wrapper around ImageProcessor
class	Morphology3DAlgorithm Wrapper around ImageProcessor
class	MorphologyBinary2DAlgorithm Wrapper around ImageProcessor
class	MorphologyFillHoles2DAlgorithm Wrapper around ImageProcessor
class	MorphologyInternalGradient2DAlgorithm Wrapper around ImageProcessor
class	MorphologyOutline2DAlgorithm Wrapper around ImageProcessor
class	MorphologySkeletonize2DAlgorithm Wrapper around ImageProcessor
class	MorphologySkeletonize3DAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.morphology with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
AddBorder2DAlgorithm	Morphology2DAlgorithm.getAddBorder2DAlgorithm()
GrayscaleAttributeFiltering2DAlgorithm.Attribute	GrayscaleAttributeFiltering2DAlgorithm.getAttribute()
GrayscaleAttributeFiltering3DAlgorithm.Attribute	GrayscaleAttributeFiltering3DAlgorithm.getAttribute()
Neighborhood2D	MorphologicalReconstruction3DAlgorithm.getConnectivity()
Neighborhood2D	MorphologicalReconstruction2DAlgorithm.getConnectivity()
Neighborhood2D	GrayscaleAttributeFiltering2DAlgorithm.getConnectivity()
Neighborhood3D	GrayscaleAttributeFiltering3DAlgorithm.getConnectivity()
inra.ijpb.morphology.Strel3D.Shape	Morphology3DAlgorithm.getElement()
inra.ijpb.morphology.Strel.Shape	Morphology2DAlgorithm.getElement()
int	MorphologyBinary2DAlgorithm.getIterations()
int	GrayscaleAttributeFiltering2DAlgorithm.getMinimumValue()
int	GrayscaleAttributeFiltering3DAlgorithm.getMinVoxelNumber()
inra.ijpb.morphology.Morphology.Operation	Morphology3DAlgorithm.getOperation()
MorphologyBinary2DAlgorithm.Operation	MorphologyBinary2DAlgorithm.getOperation()
GrayscaleAttributeFiltering2DAlgorithm.Operation	GrayscaleAttributeFiltering2DAlgorithm.getOperation()
inra.ijpb.morphology.Morphology.Operation	Morphology2DAlgorithm.getOperation()
GrayscaleAttributeFiltering3DAlgorithm.Operation	GrayscaleAttributeFiltering3DAlgorithm.getOperation()
int	Morphology3DAlgorithm.getRadius()
double	MorphologyInternalGradient2DAlgorithm.getRadius()
int	Morphology2DAlgorithm.getRadius()
boolean	Morphology2DAlgorithm.isAddBorder()
boolean	MorphologicalReconstruction3DAlgorithm.isApplyDilation()
boolean	MorphologicalReconstruction2DAlgorithm.isApplyDilation()
boolean	FindHoles2DAlgorithm.isBlackBackground()
boolean	MorphologyFillHoles2DAlgorithm.isBlackBackground()
boolean	MorphologySkeletonize2DAlgorithm.isDarkBackground()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.noise

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.noise with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AddNoise2DAlgorithm Wrapper around ImageProcessor
class	AddSaltAndPepperNoise2DAlgorithm Wrapper around ImageProcessor
class	DespeckleFilter2DAlgorithm Wrapper around RankFilters
class	RemoveOutliersFilter2DAlgorithm Wrapper around RankFilters

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.noise with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
RemoveOutliersFilter2DAlgorithm.Mode	RemoveOutliersFilter2DAlgorithm.getMode()
double	AddSaltAndPepperNoise2DAlgorithm.getPercent()
double	RemoveOutliersFilter2DAlgorithm.getRadius()
double	AddNoise2DAlgorithm.getSigma()
float	RemoveOutliersFilter2DAlgorithm.getThreshold()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.opticalflow

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.opticalflow with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	MSEBlockFlowAlgorithm Adapted from MSEBlockFlow, as the methods there are all protected/private
class	MSEGaussianFlowAlgorithm Adapted from MSEGaussianFlow, as the methods there are all protected/private
class	PMCCBlockFlowAlgorithm Adapted from PMCCBlockFlow, as the methods there are all protected/private

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.opticalflow with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	PMCCBlockFlowAlgorithm.getBlockRadius()
int	MSEBlockFlowAlgorithm.getBlockRadius()
int	MSEGaussianFlowAlgorithm.getMaxDistance()
int	PMCCBlockFlowAlgorithm.getMaxDistance()
int	MSEBlockFlowAlgorithm.getMaxDistance()
int	MSEGaussianFlowAlgorithm.getSigma()
boolean	MSEGaussianFlowAlgorithm.isAddLastIdentityField()
boolean	PMCCBlockFlowAlgorithm.isAddLastIdentityField()
boolean	MSEBlockFlowAlgorithm.isAddLastIdentityField()
boolean	MSEGaussianFlowAlgorithm.isOutputPolarCoordinates()
boolean	PMCCBlockFlowAlgorithm.isOutputPolarCoordinates()
boolean	MSEBlockFlowAlgorithm.isOutputPolarCoordinates()
boolean	MSEGaussianFlowAlgorithm.isRelativeDistances()
boolean	PMCCBlockFlowAlgorithm.isRelativeDistances()
boolean	MSEBlockFlowAlgorithm.isRelativeDistances()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.overlay

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.overlay with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ExtractOverlayAlgorithm
class	RemoveOverlayAlgorithm
class	RenderOverlayAlgorithm Wrapper around RoiDrawer
class	SetOverlayAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.overlay with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ROIElementDrawingMode	RenderOverlayAlgorithm.getDrawFilledOutlineMode()
RoiLabel	RenderOverlayAlgorithm.getDrawnLabel()
ROIElementDrawingMode	RenderOverlayAlgorithm.getDrawOutlineMode()
OptionalColorParameter	RenderOverlayAlgorithm.getLabelBackground()
Color	RenderOverlayAlgorithm.getLabelForeground()
int	RenderOverlayAlgorithm.getLabelSize()
double	RenderOverlayAlgorithm.getMagnification()
double	RenderOverlayAlgorithm.getOpacity()
OptionalColorParameter	RenderOverlayAlgorithm.getOverrideFillColor()
OptionalColorParameter	RenderOverlayAlgorithm.getOverrideLineColor()
OptionalDoubleParameter	RenderOverlayAlgorithm.getOverrideLineWidth()
boolean	RenderOverlayAlgorithm.isIgnoreC()
boolean	RenderOverlayAlgorithm.isIgnoreT()
boolean	RenderOverlayAlgorithm.isIgnoreZ()
boolean	RenderOverlayAlgorithm.isPreferRenderViaOverlay()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CropToRoiAlgorithm
class	ExtractImageInRoiAlgorithm
class	GetRoiImageAlgorithm Wrapper around RoiManager
class	RoiCalculatorAlgorithm Wrapper around RoiManager
class	SetRoiImageAlgorithm Wrapper around RoiManager
class	SplitRoiConnectedComponentsAlgorithm
class	UnsetRoiImageAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalAnnotationNameParameter	ExtractImageInRoiAlgorithm.getAnnotationCLocation()
OptionalAnnotationNameParameter	ExtractImageInRoiAlgorithm.getAnnotationTLocation()
OptionalAnnotationNameParameter	ExtractImageInRoiAlgorithm.getAnnotationXLocation()
OptionalAnnotationNameParameter	ExtractImageInRoiAlgorithm.getAnnotationYLocation()
OptionalAnnotationNameParameter	ExtractImageInRoiAlgorithm.getAnnotationZLocation()
OptionalAnnotationNameParameter	SplitRoiConnectedComponentsAlgorithm.getComponentNameAnnotation()
SplitRoiConnectedComponentsAlgorithm.DimensionOperation	SplitRoiConnectedComponentsAlgorithm.getDimensionCOperation()
SplitRoiConnectedComponentsAlgorithm.DimensionOperation	SplitRoiConnectedComponentsAlgorithm.getDimensionTOperation()
SplitRoiConnectedComponentsAlgorithm.DimensionOperation	SplitRoiConnectedComponentsAlgorithm.getDimensionZOperation()
DefaultExpressionParameter	SplitRoiConnectedComponentsAlgorithm.getGraphPostprocessing()
LogicalOperation	RoiCalculatorAlgorithm.getOperation()
DefaultExpressionParameter	SplitRoiConnectedComponentsAlgorithm.getOverlapFilter()
ImageStatisticsSetParameter	SplitRoiConnectedComponentsAlgorithm.getOverlapFilterMeasurements()
boolean	RoiCalculatorAlgorithm.isApplyPerChannel()
boolean	RoiCalculatorAlgorithm.isApplyPerFrame()
boolean	RoiCalculatorAlgorithm.isApplyPerSlice()
boolean	CropToRoiAlgorithm.isCropC()
boolean	CropToRoiAlgorithm.isCropT()
boolean	CropToRoiAlgorithm.isCropXY()
boolean	CropToRoiAlgorithm.isCropZ()
boolean	ExtractImageInRoiAlgorithm.isIgnoreC()
boolean	ExtractImageInRoiAlgorithm.isIgnoreT()
boolean	ExtractImageInRoiAlgorithm.isIgnoreZ()
boolean	SplitRoiConnectedComponentsAlgorithm.isMeasureInPhysicalUnits()
boolean	RoiCalculatorAlgorithm.isSplitAfterwards()
boolean	SplitRoiConnectedComponentsAlgorithm.isSplitAtJunctions()
boolean	SplitRoiConnectedComponentsAlgorithm.isTrySolveJunctions()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.annotations

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.annotations with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	RoiPropertiesToAnnotationsAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.annotations with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeTextAnnotationMergeMode	RoiPropertiesToAnnotationsAlgorithm.getAnnotationMergeStrategy()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getCountAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getFillColorAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getLineColorAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getLineWidthAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getLocationCAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getLocationTAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getLocationXAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getLocationYAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getLocationZAnnotation()
OptionalAnnotationNameParameter	RoiPropertiesToAnnotationsAlgorithm.getNameAnnotation()
boolean	RoiPropertiesToAnnotationsAlgorithm.isDeduplicate()
boolean	RoiPropertiesToAnnotationsAlgorithm.isOnlyFirst()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.assemble

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.assemble with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AssembleExtractedROIAlgorithm
class	ExtractFromROIAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.assemble with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalAnnotationNameParameter	ExtractFromROIAlgorithm.getAnnotationBoundingHeight()
OptionalAnnotationNameParameter	ExtractFromROIAlgorithm.getAnnotationBoundingWidth()
OptionalStringParameter	AssembleExtractedROIAlgorithm.getAnnotationC()
OptionalAnnotationNameParameter	ExtractFromROIAlgorithm.getAnnotationC()
JIPipeTextAnnotationMergeMode	ExtractFromROIAlgorithm.getAnnotationMergeStrategy()
OptionalStringParameter	AssembleExtractedROIAlgorithm.getAnnotationT()
OptionalAnnotationNameParameter	ExtractFromROIAlgorithm.getAnnotationT()
String	AssembleExtractedROIAlgorithm.getAnnotationX()
OptionalAnnotationNameParameter	ExtractFromROIAlgorithm.getAnnotationX()
String	AssembleExtractedROIAlgorithm.getAnnotationY()
OptionalAnnotationNameParameter	ExtractFromROIAlgorithm.getAnnotationY()
OptionalStringParameter	AssembleExtractedROIAlgorithm.getAnnotationZ()
OptionalAnnotationNameParameter	ExtractFromROIAlgorithm.getAnnotationZ()
OptionalColorParameter	ExtractFromROIAlgorithm.getOutsideColor()
Anchor	AssembleExtractedROIAlgorithm.getXyAnchor()
Anchor	ExtractFromROIAlgorithm.getXyAnchor()
boolean	AssembleExtractedROIAlgorithm.isDoScaling()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.convert

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.convert with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ROIToLabelsByNameAlgorithm
class	ROIToLabelsExpressionAlgorithm
class	RoiToMaskAlgorithm Wrapper around RoiManager
class	RoiToRGBAlgorithm Wrapper around RoiDrawer
class	UnreferencedRoiToMaskAlgorithm Wrapper around RoiManager
class	UnreferencedRoiToRGBAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.convert with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ROIElementDrawingMode	RoiToRGBAlgorithm.getDrawFilledOutlineMode()
ROIElementDrawingMode	UnreferencedRoiToRGBAlgorithm.getDrawFilledOutlineMode()
RoiLabel	RoiToRGBAlgorithm.getDrawnLabel()
ROIElementDrawingMode	RoiToRGBAlgorithm.getDrawOutlineMode()
ROIElementDrawingMode	UnreferencedRoiToRGBAlgorithm.getDrawOutlineMode()
Margin	UnreferencedRoiToRGBAlgorithm.getImageArea()
Margin	UnreferencedRoiToMaskAlgorithm.getImageArea()
int	ROIToLabelsByNameAlgorithm.ROINameToLabelEntry.getLabel()
ParameterCollectionList	ROIToLabelsByNameAlgorithm.getLabelAssignment()
OptionalColorParameter	RoiToRGBAlgorithm.getLabelBackground()
FontFamilyParameter	RoiToRGBAlgorithm.getLabelFontFamily()
Color	RoiToRGBAlgorithm.getLabelForeground()
int	RoiToRGBAlgorithm.getLabelSize()
int	RoiToMaskAlgorithm.getLineThickness()
int	UnreferencedRoiToMaskAlgorithm.getLineThickness()
double	RoiToRGBAlgorithm.getMagnification()
String	ROIToLabelsByNameAlgorithm.ROINameToLabelEntry.getName()
double	RoiToRGBAlgorithm.getOpacity()
OptionalColorParameter	RoiToRGBAlgorithm.getOverrideFillColor()
OptionalColorParameter	UnreferencedRoiToRGBAlgorithm.getOverrideFillColor()
OptionalColorParameter	RoiToRGBAlgorithm.getOverrideLineColor()
OptionalColorParameter	UnreferencedRoiToRGBAlgorithm.getOverrideLineColor()
OptionalDoubleParameter	RoiToRGBAlgorithm.getOverrideLineWidth()
OptionalDoubleParameter	UnreferencedRoiToRGBAlgorithm.getOverrideLineWidth()
OptionalDefaultExpressionParameter	ROIToLabelsExpressionAlgorithm.getRoiToLabelTransformation()
boolean	RoiToMaskAlgorithm.isDrawFilledOutline()
boolean	UnreferencedRoiToMaskAlgorithm.isDrawFilledOutline()
boolean	UnreferencedRoiToRGBAlgorithm.isDrawLabel()
boolean	RoiToMaskAlgorithm.isDrawOutline()
boolean	ROIToLabelsExpressionAlgorithm.isDrawOutline()
boolean	ROIToLabelsByNameAlgorithm.isDrawOutline()
boolean	UnreferencedRoiToMaskAlgorithm.isDrawOutline()
boolean	RoiToRGBAlgorithm.isDrawOver()
boolean	UnreferencedRoiToRGBAlgorithm.isDrawOver()
boolean	RoiToMaskAlgorithm.isDrawOver()
boolean	ROIToLabelsExpressionAlgorithm.isFillOutline()
boolean	ROIToLabelsByNameAlgorithm.isFillOutline()
boolean	RoiToRGBAlgorithm.isIgnoreC()
boolean	UnreferencedRoiToRGBAlgorithm.isIgnoreC()
boolean	RoiToRGBAlgorithm.isIgnoreT()
boolean	UnreferencedRoiToRGBAlgorithm.isIgnoreT()
boolean	RoiToRGBAlgorithm.isIgnoreZ()
boolean	UnreferencedRoiToRGBAlgorithm.isIgnoreZ()
boolean	UnreferencedRoiToRGBAlgorithm.isPreferAssociatedImage()
boolean	UnreferencedRoiToMaskAlgorithm.isPreferAssociatedImage()
boolean	RoiToRGBAlgorithm.isPreferRenderViaOverlay()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.draw

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.draw with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DrawOvalRoiAlgorithm
class	DrawRectangleRoiAlgorithm
class	DrawScaleBarRoiAlgorithm
class	DrawTextRoiAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.draw with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
double	DrawTextRoiAlgorithm.getAngle()
int	DrawRectangleRoiAlgorithm.getArcHeight()
int	DrawRectangleRoiAlgorithm.getArcWidth()
OptionalColorParameter	DrawScaleBarRoiAlgorithm.getBackgroundColor()
Color	DrawScaleBarRoiAlgorithm.getBarColor()
int	DrawScaleBarRoiAlgorithm.getBarThickness()
OptionalColorParameter	ROIProperties.getFillColor()
FontFamilyParameter	DrawScaleBarRoiAlgorithm.TextSettings.getFontFamily()
FontFamilyParameter	DrawTextRoiAlgorithm.getFontFamily()
int	DrawScaleBarRoiAlgorithm.TextSettings.getFontSize()
int	DrawTextRoiAlgorithm.getFontSize()
FontStyleParameter	DrawScaleBarRoiAlgorithm.TextSettings.getFontStyle()
FontStyleParameter	DrawTextRoiAlgorithm.getFontStyle()
OptionalQuantity	DrawScaleBarRoiAlgorithm.getHorizontalBarSize()
DefaultExpressionParameter	DrawScaleBarRoiAlgorithm.TextSettings.getHorizontalLabel()
OptionalColorParameter	ROIProperties.getLineColor()
double	ROIProperties.getLineWidth()
ScaleBarGenerator.ScaleBarPosition	DrawScaleBarRoiAlgorithm.getLocation()
FixedMargin	DrawTextRoiAlgorithm.getLocation()
int	ROIProperties.getPositionC()
int	ROIProperties.getPositionT()
int	ROIProperties.getPositionZ()
Margin.List	DrawRectangleRoiAlgorithm.getRectangles()
Margin.List	DrawOvalRoiAlgorithm.getRectangles()
DefaultExpressionParameter	ROIProperties.getRoiName()
ROIProperties	DrawRectangleRoiAlgorithm.getRoiProperties()
ROIProperties	DrawOvalRoiAlgorithm.getRoiProperties()
ROIProperties	DrawTextRoiAlgorithm.getRoiProperties()
DefaultExpressionParameter	DrawTextRoiAlgorithm.getText()
Color	DrawScaleBarRoiAlgorithm.TextSettings.getTextColor()
DrawScaleBarRoiAlgorithm.TextSettings	DrawScaleBarRoiAlgorithm.getTextSettings()
OptionalQuantity	DrawScaleBarRoiAlgorithm.getVerticalBarSize()
DefaultExpressionParameter	DrawScaleBarRoiAlgorithm.TextSettings.getVerticalLabel()
boolean	DrawTextRoiAlgorithm.isAntialiased()
boolean	DrawRectangleRoiAlgorithm.isCenter()
boolean	DrawOvalRoiAlgorithm.isCenter()
boolean	DrawTextRoiAlgorithm.isCenter()
boolean	DrawScaleBarRoiAlgorithm.isDrawHorizontal()
boolean	DrawScaleBarRoiAlgorithm.isDrawVertical()
boolean	DrawScaleBarRoiAlgorithm.TextSettings.isHideLabels()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.filter

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.filter with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	FilterRoiByNameAlgorithm Wrapper around RoiManager
class	FilterROIByOverlapAlgorithm
class	FilterRoiByStatisticsAlgorithm Wrapper around RoiManager
class	FilterRoiByStatisticsScriptAlgorithm Wrapper around RoiManager
class	FilterROIListsAlgorithm
class	RemoveBorderRoisAlgorithm Wrapper around RoiManager
class	SliceROIListAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.filter with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Margin	RemoveBorderRoisAlgorithm.getBorderDefinition()
PythonScript	FilterRoiByStatisticsScriptAlgorithm.getCode()
CustomExpressionVariablesParameter	FilterRoiByStatisticsAlgorithm.getCustomFilterVariables()
CustomExpressionVariablesParameter	FilterROIByOverlapAlgorithm.getCustomVariables()
DefaultExpressionParameter	FilterROIListsAlgorithm.getFilter()
DefaultExpressionParameter	FilterRoiByStatisticsAlgorithm.getFilters()
DefaultExpressionParameter	FilterRoiByNameAlgorithm.getFilters()
ImageStatisticsSetParameter	FilterRoiByStatisticsAlgorithm.getMeasurements()
RoiOutline	RemoveBorderRoisAlgorithm.getOutline()
DefaultExpressionParameter	FilterROIByOverlapAlgorithm.ROIFilterSettings.getOverlapFilter()
ImageStatisticsSetParameter	FilterROIByOverlapAlgorithm.getOverlapFilterMeasurements()
FilterROIByOverlapAlgorithm.ROIFilterSettings	FilterROIByOverlapAlgorithm.getRoi1Settings()
FilterROIByOverlapAlgorithm.ROIFilterSettings	FilterROIByOverlapAlgorithm.getRoi2Settings()
JIPipeDynamicParameterCollection	FilterRoiByStatisticsScriptAlgorithm.getScriptParameters()
IntegerRange	SliceROIListAlgorithm.getSelectedIndices()
boolean	SliceROIListAlgorithm.isAutoClamp()
boolean	FilterROIByOverlapAlgorithm.ROIFilterSettings.isConsumeOnOverlap()
boolean	FilterROIByOverlapAlgorithm.ROIFilterSettings.isEnabled()
boolean	FilterROIByOverlapAlgorithm.ROIFilterSettings.isFastMode()
boolean	FilterROIListsAlgorithm.isIncludeAnnotations()
boolean	FilterROIByOverlapAlgorithm.ROIFilterSettings.isInvert()
boolean	FilterRoiByStatisticsAlgorithm.isMeasureInPhysicalUnits()
boolean	FilterROIByOverlapAlgorithm.ROIFilterSettings.isMeasureInPhysicalUnits()
boolean	FilterRoiByStatisticsAlgorithm.isOutputEmptyLists()
boolean	FilterRoiByNameAlgorithm.isOutputEmptyLists()
boolean	FilterROIListsAlgorithm.isOutputEmptyLists()
boolean	FilterROIByOverlapAlgorithm.ROIFilterSettings.isOutputOverlaps()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.generate

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.generate with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AppendRectangularRoiAlgorithm Deprecated.
class	DefineRectangularRoiAlgorithm Deprecated.
class	GenerateMissingRoiListsAlgorithm
class	MaskToRoiAlgorithm
class	ReferencedAppendRectangularRoiAlgorithm Deprecated.
class	ReferencedDefineRectangularRoiAlgorithm Deprecated.
class	TableToCircularROIAlgorithm Wrapper around RoiManager
class	TableToRectangularROIAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.generate with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnC()
TableColumnSourceExpressionParameter	TableToCircularROIAlgorithm.getColumnC()
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnHeight()
TableColumnSourceExpressionParameter	TableToCircularROIAlgorithm.getColumnRadius()
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnT()
TableColumnSourceExpressionParameter	TableToCircularROIAlgorithm.getColumnT()
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnWidth()
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnX1()
TableColumnSourceExpressionParameter	TableToCircularROIAlgorithm.getColumnX1()
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnX2()
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnY1()
TableColumnSourceExpressionParameter	TableToCircularROIAlgorithm.getColumnY1()
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnY2()
TableColumnSourceExpressionParameter	TableToRectangularROIAlgorithm.getColumnZ()
TableColumnSourceExpressionParameter	TableToCircularROIAlgorithm.getColumnZ()
TableToRectangularROIAlgorithm.Mode	TableToRectangularROIAlgorithm.getMode()
Margin.List	AppendRectangularRoiAlgorithm.getRectangles() Deprecated.
RectangleList	DefineRectangularRoiAlgorithm.getRectangles() Deprecated.
Margin.List	ReferencedAppendRectangularRoiAlgorithm.getRectangles() Deprecated.
Margin.List	ReferencedDefineRectangularRoiAlgorithm.getRectangles() Deprecated.
int	MaskToRoiAlgorithm.getThreshold()
boolean	MaskToRoiAlgorithm.isInvertThreshold()
boolean	TableToRectangularROIAlgorithm.isOneBasedPositions()
boolean	TableToCircularROIAlgorithm.isOneBasedPositions()
boolean	DefineRectangularRoiAlgorithm.isSplit() Deprecated.
boolean	ReferencedDefineRectangularRoiAlgorithm.isSplit() Deprecated.
void	TableToRectangularROIAlgorithm.setAnchor(TableToRectangularROIAlgorithm.Anchor anchor)

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.measure

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.measure with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	CountROIAlgorithm
class	RoiStatisticsAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.measure with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalStringParameter	RoiStatisticsAlgorithm.getIndexAnnotation()
ImageStatisticsSetParameter	RoiStatisticsAlgorithm.getMeasurements()
boolean	CountROIAlgorithm.isAddAnnotations()
boolean	RoiStatisticsAlgorithm.isAddNameToTable()
boolean	RoiStatisticsAlgorithm.isApplyPerChannel()
boolean	RoiStatisticsAlgorithm.isApplyPerFrame()
boolean	RoiStatisticsAlgorithm.isApplyPerSlice()
boolean	RoiStatisticsAlgorithm.isMeasureInPhysicalUnits()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.merge

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.merge with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AddRoiListsAlgorithm Wrapper around RoiManager
class	FilterAndMergeRoiByStatisticsScriptAlgorithm Wrapper around RoiManager
class	MergeRoiListsAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.merge with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
PythonScript	FilterAndMergeRoiByStatisticsScriptAlgorithm.getCode()
JIPipeDynamicParameterCollection	FilterAndMergeRoiByStatisticsScriptAlgorithm.getScriptParameters()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.modify

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.modify with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ChangeRoiNameFromExpressionsAndMeasurementsAlgorithm
class	ChangeRoiPropertiesAlgorithm Wrapper around RoiManager
class	ChangeRoiPropertiesFromAnnotationsAlgorithm Wrapper around RoiManager
class	ChangeRoiPropertiesFromExpressionsAlgorithm Wrapper around RoiManager
class	ColorRoiByNameAlgorithm
class	ColorRoiByStatisticsAlgorithm Wrapper around RoiManager
class	OutlineRoiAlgorithm Wrapper around RoiManager
class	ReorderRoiDimensionsAlgorithm Algorithm that reorders Hyperstack dimensions
class	RoiFloodFillAlgorithm Wrapper around RoiManager
class	RoiToCentroidAlgorithm Wrapper around RoiManager
class	ScaleRoiAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.modify with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getCenterScale()
boolean	ChangeRoiPropertiesAlgorithm.getCenterScale()
boolean	ScaleRoiAlgorithm.getCenterScale()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getCenterScale()
CustomExpressionVariablesParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getCustomFilterVariables()
StringQueryExpression	ChangeRoiNameFromExpressionsAndMeasurementsAlgorithm.getExpression()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getFillColor()
OptionalColorParameter	ChangeRoiPropertiesAlgorithm.getFillColor()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getFillColor()
MeasurementColumn	ColorRoiByStatisticsAlgorithm.getFillMeasurement()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getLineColor()
OptionalColorParameter	ChangeRoiPropertiesAlgorithm.getLineColor()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getLineColor()
MeasurementColumn	ColorRoiByStatisticsAlgorithm.getLineMeasurement()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getLineWidth()
OptionalDoubleParameter	ChangeRoiPropertiesAlgorithm.getLineWidth()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getLineWidth()
OptionalColorMapParameter	ColorRoiByStatisticsAlgorithm.getMapFillColor()
OptionalColorMapParameter	ColorRoiByNameAlgorithm.getMapFillColor()
OptionalColorMapParameter	ColorRoiByStatisticsAlgorithm.getMapLineColor()
OptionalColorMapParameter	ColorRoiByNameAlgorithm.getMapLineColor()
ImageStatisticsSetParameter	ChangeRoiNameFromExpressionsAndMeasurementsAlgorithm.getMeasurements()
ImageStatisticsSetParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getMeasurements()
RoiFloodFillAlgorithm.Mode	RoiFloodFillAlgorithm.getMode()
RoiOutline	OutlineRoiAlgorithm.getOutline()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getPositionC()
OptionalIntegerParameter	ChangeRoiPropertiesAlgorithm.getPositionC()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getPositionC()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getPositionT()
OptionalIntegerParameter	ChangeRoiPropertiesAlgorithm.getPositionT()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getPositionT()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getPositionX()
OptionalDoubleParameter	ChangeRoiPropertiesAlgorithm.getPositionX()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getPositionX()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getPositionY()
OptionalDoubleParameter	ChangeRoiPropertiesAlgorithm.getPositionY()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getPositionY()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getPositionZ()
OptionalIntegerParameter	ChangeRoiPropertiesAlgorithm.getPositionZ()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getPositionZ()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getRoiName()
OptionalStringParameter	ChangeRoiPropertiesAlgorithm.getRoiName()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getRoiName()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getScaleX()
OptionalDoubleParameter	ChangeRoiPropertiesAlgorithm.getScaleX()
double	ScaleRoiAlgorithm.getScaleX()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getScaleX()
OptionalAnnotationNameParameter	ChangeRoiPropertiesFromAnnotationsAlgorithm.getScaleY()
OptionalDoubleParameter	ChangeRoiPropertiesAlgorithm.getScaleY()
double	ScaleRoiAlgorithm.getScaleY()
OptionalDefaultExpressionParameter	ChangeRoiPropertiesFromExpressionsAlgorithm.getScaleY()
HyperstackDimension	ReorderRoiDimensionsAlgorithm.getTargetC()
HyperstackDimension	ReorderRoiDimensionsAlgorithm.getTargetT()
HyperstackDimension	ReorderRoiDimensionsAlgorithm.getTargetZ()
double	RoiFloodFillAlgorithm.getTolerance()
boolean	ChangeRoiNameFromExpressionsAndMeasurementsAlgorithm.isIncludeAnnotations()
boolean	ChangeRoiNameFromExpressionsAndMeasurementsAlgorithm.isMeasureInPhysicalUnits()
boolean	ChangeRoiPropertiesFromExpressionsAlgorithm.isMeasureInPhysicalUnits()
boolean	RoiFloodFillAlgorithm.isSmooth()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.properties

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.properties with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ExtractROIMetadataAlgorithm
class	RemoveROIMetadataAlgorithm
class	SetRoiMetadataByStatisticsAlgorithm Wrapper around RoiManager
class	SetROIMetadataFromTableAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.properties with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
CustomExpressionVariablesParameter	SetRoiMetadataByStatisticsAlgorithm.getCustomVariables()
DefaultExpressionParameter	RemoveROIMetadataAlgorithm.getFilterExpression()
OptionalStringParameter	ExtractROIMetadataAlgorithm.getIndexColumn()
String	SetRoiMetadataByStatisticsAlgorithm.MetadataProperty.getKey()
ImageStatisticsSetParameter	SetRoiMetadataByStatisticsAlgorithm.getMeasurements()
ParameterCollectionList	SetRoiMetadataByStatisticsAlgorithm.getMetadataGenerators()
OptionalStringParameter	ExtractROIMetadataAlgorithm.getNameColumn()
TableColumnSourceExpressionParameter	SetROIMetadataFromTableAlgorithm.getRoiIndexColumn()
DefaultExpressionParameter	SetRoiMetadataByStatisticsAlgorithm.MetadataProperty.getValue()
boolean	SetRoiMetadataByStatisticsAlgorithm.isClearBeforeWrite()
boolean	SetROIMetadataFromTableAlgorithm.isClearBeforeWrite()
boolean	SetRoiMetadataByStatisticsAlgorithm.isMeasureInPhysicalUnits()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.sort

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.sort with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	SortAndExtractRoiByStatisticsAlgorithm Deprecated.
class	SortAndExtractRoiByStatisticsAlgorithm2 Wrapper around RoiManager
class	SortRoiListByExpressionsAndMeasurementsAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.sort with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
CustomExpressionVariablesParameter	SortRoiListByExpressionsAndMeasurementsAlgorithm.getCustomFilterVariables()
StringQueryExpression	SortRoiListByExpressionsAndMeasurementsAlgorithm.getExpression()
OptionalColorMapParameter	SortAndExtractRoiByStatisticsAlgorithm.getMapFillColor() Deprecated.
OptionalColorMapParameter	SortAndExtractRoiByStatisticsAlgorithm2.getMapFillColor()
OptionalColorMapParameter	SortAndExtractRoiByStatisticsAlgorithm.getMapLineColor() Deprecated.
OptionalColorMapParameter	SortAndExtractRoiByStatisticsAlgorithm2.getMapLineColor()
ImageStatisticsSetParameter	SortRoiListByExpressionsAndMeasurementsAlgorithm.getMeasurements()
OptionalIntegerRange	SortAndExtractRoiByStatisticsAlgorithm2.getSelectedIndices()
NumericFunctionExpression	SortAndExtractRoiByStatisticsAlgorithm.getSelection() Deprecated.
MeasurementColumnSortOrder.List	SortAndExtractRoiByStatisticsAlgorithm.getSortOrderList() Deprecated.
MeasurementColumnSortOrder.List	SortAndExtractRoiByStatisticsAlgorithm2.getSortOrderList()
boolean	SortAndExtractRoiByStatisticsAlgorithm.isAutoClamp() Deprecated.
boolean	SortAndExtractRoiByStatisticsAlgorithm2.isAutoClamp()
boolean	SortRoiListByExpressionsAndMeasurementsAlgorithm.isIncludeAnnotations()
boolean	SortRoiListByExpressionsAndMeasurementsAlgorithm.isMeasureInPhysicalUnits()
boolean	SortRoiListByExpressionsAndMeasurementsAlgorithm.isReverseSortOrder()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.split

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.split with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ExplodeRoiAlgorithm Wrapper around RoiManager
class	SplitRoiAlgorithm Wrapper around RoiManager

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.roi.split with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DefaultExpressionParameter	ExplodeRoiAlgorithm.getAnnotationValue()
CustomExpressionVariablesParameter	ExplodeRoiAlgorithm.getCustomExpressionVariables()
OptionalStringParameter	ExplodeRoiAlgorithm.getGeneratedAnnotation()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.segment

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.segment with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ClassicWatershedSegmentationAlgorithm
class	RidgeDetector2DAlgorithm
class	SeededWatershedSegmentationAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.segment with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Neighborhood2D3D	SeededWatershedSegmentationAlgorithm.getConnectivity()
Neighborhood2D3D	ClassicWatershedSegmentationAlgorithm.getConnectivity()
double	RidgeDetector2DAlgorithm.getContrastHigh()
double	RidgeDetector2DAlgorithm.getContrastLow()
OptionalDoubleParameter	ClassicWatershedSegmentationAlgorithm.getCustomHMax()
OptionalDoubleParameter	ClassicWatershedSegmentationAlgorithm.getCustomHMin()
double	RidgeDetector2DAlgorithm.getLineWidth()
double	RidgeDetector2DAlgorithm.getLowerThreshold()
double	RidgeDetector2DAlgorithm.getMaxLength()
double	RidgeDetector2DAlgorithm.getMinLength()
de.biomedical_imaging.ij.steger.OverlapOption	RidgeDetector2DAlgorithm.getOverlapResolution()
double	RidgeDetector2DAlgorithm.getSigma()
ImageROITargetArea	SeededWatershedSegmentationAlgorithm.getTargetArea()
ImageROITargetArea	ClassicWatershedSegmentationAlgorithm.getTargetArea()
double	RidgeDetector2DAlgorithm.getUpperThreshold()
boolean	SeededWatershedSegmentationAlgorithm.isApplyPerSlice()
boolean	ClassicWatershedSegmentationAlgorithm.isApplyPerSlice()
boolean	RidgeDetector2DAlgorithm.isDarkLine()
boolean	RidgeDetector2DAlgorithm.isDoCorrectPosition()
boolean	RidgeDetector2DAlgorithm.isDoEstimateWidth()
boolean	RidgeDetector2DAlgorithm.isDoExtendLine()
boolean	RidgeDetector2DAlgorithm.isEstimateHighThreshold()
boolean	RidgeDetector2DAlgorithm.isEstimateLowThreshold()
boolean	RidgeDetector2DAlgorithm.isEstimateSigma()
boolean	SeededWatershedSegmentationAlgorithm.isGetDams()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.sharpen

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.sharpen with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	LaplacianSharpen2DAlgorithm Wrapper around ImageProcessor

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.statistics

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.statistics with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AverageKeyValueThresholdStatisticsGenerator
class	FastKeyValueThresholdStatisticsGenerator
class	HistogramGenerator Algorithm that generates ResultsTableData as histogram
class	KeyValueAveragesGenerator
class	KeyValueHistogramGenerator
class	KeyValueThresholdPartitionAveragesGenerator
class	KeyValueThresholdPartitionGenerator
class	KeyValueThresholdStatisticsGenerator

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.statistics with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalStringParameter	KeyValueThresholdPartitionAveragesGenerator.getClass0CountColumnName()
OptionalStringParameter	KeyValueThresholdPartitionAveragesGenerator.getClass0MeanColumnName()
OptionalStringParameter	KeyValueThresholdPartitionAveragesGenerator.getClass0SumColumnName()
OptionalStringParameter	KeyValueThresholdPartitionAveragesGenerator.getClass1CountColumnName()
OptionalStringParameter	KeyValueThresholdPartitionAveragesGenerator.getClass1MeanColumnName()
OptionalStringParameter	KeyValueThresholdPartitionAveragesGenerator.getClass1SumColumnName()
OptionalStringParameter	KeyValueAveragesGenerator.getCountColumnName()
ParameterCollectionList	KeyValueThresholdPartitionGenerator.getGeneratedColumns()
DefaultExpressionParameter	KeyValueHistogramGenerator.getIntegrationFunction()
DefaultExpressionParameter	KeyValueThresholdStatisticsGenerator.getIntegrationFunctionBackground()
TableColumnIntegrationParameter	FastKeyValueThresholdStatisticsGenerator.getIntegrationFunctionBackground()
DefaultExpressionParameter	KeyValueThresholdStatisticsGenerator.getIntegrationFunctionForeground()
TableColumnIntegrationParameter	FastKeyValueThresholdStatisticsGenerator.getIntegrationFunctionForeground()
OptionalStringParameter	KeyValueThresholdPartitionAveragesGenerator.getKeyColumnName()
OptionalStringParameter	KeyValueAveragesGenerator.getKeyColumnName()
OptionalStringParameter	KeyValueAveragesGenerator.getMeanColumnName()
HistogramGenerator.MultiChannelMode	HistogramGenerator.getMultiChannelMode()
String	KeyValueThresholdPartitionGenerator.GeneratedColumn.getName()
String	AverageKeyValueThresholdStatisticsGenerator.getOutputBackgroundColumn()
String	KeyValueThresholdStatisticsGenerator.getOutputBackgroundColumn()
String	FastKeyValueThresholdStatisticsGenerator.getOutputBackgroundColumn()
String	AverageKeyValueThresholdStatisticsGenerator.getOutputForegroundColumn()
String	KeyValueThresholdStatisticsGenerator.getOutputForegroundColumn()
String	FastKeyValueThresholdStatisticsGenerator.getOutputForegroundColumn()
String	KeyValueHistogramGenerator.getOutputKeyColumn()
String	AverageKeyValueThresholdStatisticsGenerator.getOutputThresholdColumn()
String	KeyValueThresholdStatisticsGenerator.getOutputThresholdColumn()
String	FastKeyValueThresholdStatisticsGenerator.getOutputThresholdColumn()
String	KeyValueHistogramGenerator.getOutputValueColumn()
String	HistogramGenerator.getSliceAnnotation()
ImageROITargetArea	KeyValueThresholdPartitionAveragesGenerator.getSourceArea()
ImageROITargetArea	KeyValueAveragesGenerator.getSourceArea()
ImageROITargetArea	KeyValueHistogramGenerator.getSourceArea()
ImageROITargetArea	KeyValueThresholdPartitionGenerator.getSourceArea()
OptionalStringParameter	KeyValueAveragesGenerator.getSumColumnName()
DefaultExpressionParameter	KeyValueThresholdPartitionGenerator.GeneratedColumn.getValue()
boolean	HistogramGenerator.isApplyPerSlice()
boolean	KeyValueHistogramGenerator.isCumulative()
boolean	AverageKeyValueThresholdStatisticsGenerator.isInvertThreshold()
boolean	KeyValueThresholdStatisticsGenerator.isInvertThreshold()
boolean	FastKeyValueThresholdStatisticsGenerator.isInvertThreshold()
boolean	HistogramGenerator.isNormalize()
boolean	KeyValueHistogramGenerator.isNormalize()
boolean	KeyValueThresholdPartitionGenerator.GeneratedColumn.isSkipEmpty()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AutoThreshold2DAlgorithm Thresholding node that thresholds via an auto threshold
class	BrightSpotsSegmentation2DAlgorithm Applies Bright spots segmentation
class	CircularHoughSegmentation2DAlgorithm Segments using a Hough circle transform
class	CustomAutoThreshold2D16UAlgorithm Thresholding node that thresholds via an auto threshold
class	CustomAutoThreshold2D32FAlgorithm Thresholding node that thresholds via an auto threshold
class	CustomAutoThreshold2D8UAlgorithm Thresholding node that thresholds via an auto threshold
class	FastCircularHoughSegmentation2DAlgorithm Segments using a Hough circle transform This code is based on ...
class	HessianSegmentation2DAlgorithm Segments using a Hessian
class	InternalGradientSegmentation2DAlgorithm Internal gradient segmenter
class	LinesHoughDetection2DAlgorithm
class	ManualThreshold16U2DAlgorithm Wrapper around ImageProcessor
class	ManualThreshold32F2DAlgorithm Wrapper around ImageProcessor
class	ManualThreshold8U2DAlgorithm Wrapper around ImageProcessor
class	PercentileThreshold8U2DAlgorithm Wrapper around ImageProcessor
class	ThresholdByAnnotation2DAlgorithm Wrapper around ImageProcessor

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	LinesHoughDetection2DAlgorithm.getAccumulatorThreshold()
AutoThreshold2DAlgorithm	HessianSegmentation2DAlgorithm.getAutoThresholding()
AutoThreshold2DAlgorithm	InternalGradientSegmentation2DAlgorithm.getAutoThresholding()
AutoThreshold2DAlgorithm	BrightSpotsSegmentation2DAlgorithm.getAutoThresholding()
int	CircularHoughSegmentation2DAlgorithm.getBandwidth()
CLAHEContrastEnhancer	InternalGradientSegmentation2DAlgorithm.getContrastEnhancer()
int	HessianSegmentation2DAlgorithm.getDespeckleIterations()
int	BrightSpotsSegmentation2DAlgorithm.getDilationErodeSteps()
int	InternalGradientSegmentation2DAlgorithm.getDilationIterations()
EigenvalueSelection2D	HessianSegmentation2DAlgorithm.getEigenvalueSelection()
int	InternalGradientSegmentation2DAlgorithm.getErosionIterations()
double	BrightSpotsSegmentation2DAlgorithm.getGaussianSigma()
double	InternalGradientSegmentation2DAlgorithm.getGaussSigma()
double	HessianSegmentation2DAlgorithm.getGradientRadius()
int	InternalGradientSegmentation2DAlgorithm.getInternalGradientRadius()
int	CircularHoughSegmentation2DAlgorithm.getLocalRadius()
int	CircularHoughSegmentation2DAlgorithm.getMaxNumCircles()
int	FastCircularHoughSegmentation2DAlgorithm.getMaxRadius()
int	CircularHoughSegmentation2DAlgorithm.getMaxRadius()
float	ManualThreshold32F2DAlgorithm.getMaxThreshold()
OptionalAnnotationNameParameter	ManualThreshold8U2DAlgorithm.getMaxThresholdAnnotation()
OptionalAnnotationNameParameter	ManualThreshold32F2DAlgorithm.getMaxThresholdAnnotation()
OptionalAnnotationNameParameter	ManualThreshold16U2DAlgorithm.getMaxThresholdAnnotation()
OptionalAnnotationNameParameter	ThresholdByAnnotation2DAlgorithm.getMaxThresholdAnnotation()
ij.process.AutoThresholder.Method	AutoThreshold2DAlgorithm.getMethod()
int	CircularHoughSegmentation2DAlgorithm.getMinNumCircles()
int	FastCircularHoughSegmentation2DAlgorithm.getMinRadius()
int	CircularHoughSegmentation2DAlgorithm.getMinRadius()
double	FastCircularHoughSegmentation2DAlgorithm.getMinScore()
float	ManualThreshold32F2DAlgorithm.getMinThreshold()
OptionalAnnotationNameParameter	ManualThreshold8U2DAlgorithm.getMinThresholdAnnotation()
OptionalAnnotationNameParameter	ManualThreshold32F2DAlgorithm.getMinThresholdAnnotation()
OptionalAnnotationNameParameter	ManualThreshold16U2DAlgorithm.getMinThresholdAnnotation()
OptionalAnnotationNameParameter	ThresholdByAnnotation2DAlgorithm.getMinThresholdAnnotation()
double	PercentileThreshold8U2DAlgorithm.getPercentile()
OptionalFloatParameter	LinesHoughDetection2DAlgorithm.getPixelThreshold()
int	CircularHoughSegmentation2DAlgorithm.getRadiusIncrement()
double	CircularHoughSegmentation2DAlgorithm.getRatio()
int	CircularHoughSegmentation2DAlgorithm.getResolution()
DefaultExpressionParameter	LinesHoughDetection2DAlgorithm.getRoiNameExpression()
int	BrightSpotsSegmentation2DAlgorithm.getRollingBallRadius()
OptionalIntegerParameter	LinesHoughDetection2DAlgorithm.getSelectTopN()
double	HessianSegmentation2DAlgorithm.getSmoothing()
ImageROITargetArea	CustomAutoThreshold2D8UAlgorithm.getSourceArea()
ImageROITargetArea	CustomAutoThreshold2D16UAlgorithm.getSourceArea()
ImageROITargetArea	CustomAutoThreshold2D32FAlgorithm.getSourceArea()
ImageROITargetArea	AutoThreshold2DAlgorithm.getSourceArea()
IntNumberRangeParameter	ManualThreshold8U2DAlgorithm.getThreshold()
double	CircularHoughSegmentation2DAlgorithm.getThreshold()
IntNumberRangeParameter	ManualThreshold16U2DAlgorithm.getThreshold()
OptionalAnnotationNameParameter	CustomAutoThreshold2D8UAlgorithm.getThresholdAnnotation()
OptionalAnnotationNameParameter	CustomAutoThreshold2D16UAlgorithm.getThresholdAnnotation()
OptionalAnnotationNameParameter	CustomAutoThreshold2D32FAlgorithm.getThresholdAnnotation()
OptionalAnnotationNameParameter	AutoThreshold2DAlgorithm.getThresholdAnnotation()
JIPipeTextAnnotationMergeMode	CustomAutoThreshold2D8UAlgorithm.getThresholdAnnotationStrategy()
JIPipeTextAnnotationMergeMode	ManualThreshold8U2DAlgorithm.getThresholdAnnotationStrategy()
JIPipeTextAnnotationMergeMode	CustomAutoThreshold2D16UAlgorithm.getThresholdAnnotationStrategy()
JIPipeTextAnnotationMergeMode	CustomAutoThreshold2D32FAlgorithm.getThresholdAnnotationStrategy()
JIPipeTextAnnotationMergeMode	AutoThreshold2DAlgorithm.getThresholdAnnotationStrategy()
JIPipeTextAnnotationMergeMode	ManualThreshold32F2DAlgorithm.getThresholdAnnotationStrategy()
JIPipeTextAnnotationMergeMode	ManualThreshold16U2DAlgorithm.getThresholdAnnotationStrategy()
DefaultExpressionParameter	CustomAutoThreshold2D8UAlgorithm.getThresholdCalculationExpression()
DefaultExpressionParameter	CustomAutoThreshold2D16UAlgorithm.getThresholdCalculationExpression()
DefaultExpressionParameter	CustomAutoThreshold2D32FAlgorithm.getThresholdCalculationExpression()
DefaultExpressionParameter	CustomAutoThreshold2D8UAlgorithm.getThresholdCombinationExpression()
DefaultExpressionParameter	CustomAutoThreshold2D16UAlgorithm.getThresholdCombinationExpression()
DefaultExpressionParameter	CustomAutoThreshold2D32FAlgorithm.getThresholdCombinationExpression()
DefaultExpressionParameter	AutoThreshold2DAlgorithm.getThresholdCombinationExpression()
AutoThreshold2DAlgorithm.SliceThresholdMode	CustomAutoThreshold2D8UAlgorithm.getThresholdMode()
AutoThreshold2DAlgorithm.SliceThresholdMode	CustomAutoThreshold2D16UAlgorithm.getThresholdMode()
AutoThreshold2DAlgorithm.SliceThresholdMode	CustomAutoThreshold2D32FAlgorithm.getThresholdMode()
AutoThreshold2DAlgorithm.SliceThresholdMode	AutoThreshold2DAlgorithm.getThresholdMode()
boolean	CustomAutoThreshold2D8UAlgorithm.isAccessPixels()
boolean	CustomAutoThreshold2D16UAlgorithm.isAccessPixels()
boolean	CustomAutoThreshold2D32FAlgorithm.isAccessPixels()
boolean	HessianSegmentation2DAlgorithm.isApplyDespeckle()
boolean	InternalGradientSegmentation2DAlgorithm.isApplyFirstCLAHE()
boolean	InternalGradientSegmentation2DAlgorithm.isApplyGaussian()
boolean	HessianSegmentation2DAlgorithm.isApplyInternalGradient()
boolean	InternalGradientSegmentation2DAlgorithm.isApplySecondCLAHE()
boolean	HessianSegmentation2DAlgorithm.isCompareAbsolute()
boolean	AutoThreshold2DAlgorithm.isDarkBackground()
boolean	CircularHoughSegmentation2DAlgorithm.isLocal()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.color

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ColorThresholdExpression2D
class	ManualHSBThreshold2DAlgorithm
class	ManualLABThreshold2DAlgorithm
class	ManualRGBThreshold2DAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.color with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
IntNumberRangeParameter	ManualRGBThreshold2DAlgorithm.getBlueThreshold()
IntNumberRangeParameter	ManualLABThreshold2DAlgorithm.getBlueYellowThreshold()
IntNumberRangeParameter	ManualHSBThreshold2DAlgorithm.getBrightnessThreshold()
DefaultExpressionParameter	ColorThresholdExpression2D.getExpression()
IntNumberRangeParameter	ManualLABThreshold2DAlgorithm.getGreenRedThreshold()
IntNumberRangeParameter	ManualRGBThreshold2DAlgorithm.getGreenThreshold()
IntNumberRangeParameter	ManualHSBThreshold2DAlgorithm.getHueThreshold()
IntNumberRangeParameter	ManualLABThreshold2DAlgorithm.getLightnessThreshold()
OptionalAnnotationNameParameter	ManualRGBThreshold2DAlgorithm.getMaxBlueThresholdAnnotation()
OptionalAnnotationNameParameter	ManualLABThreshold2DAlgorithm.getMaxBlueYellowThresholdAnnotation()
OptionalAnnotationNameParameter	ManualHSBThreshold2DAlgorithm.getMaxBrightnessThresholdAnnotation()
OptionalAnnotationNameParameter	ManualLABThreshold2DAlgorithm.getMaxGreenRedThresholdAnnotation()
OptionalAnnotationNameParameter	ManualRGBThreshold2DAlgorithm.getMaxGreenThresholdAnnotation()
OptionalAnnotationNameParameter	ManualHSBThreshold2DAlgorithm.getMaxHueThresholdAnnotation()
OptionalAnnotationNameParameter	ManualLABThreshold2DAlgorithm.getMaxLightnessThresholdAnnotation()
OptionalAnnotationNameParameter	ManualRGBThreshold2DAlgorithm.getMaxRedThresholdAnnotation()
OptionalAnnotationNameParameter	ManualHSBThreshold2DAlgorithm.getMaxSaturationThresholdAnnotation()
OptionalAnnotationNameParameter	ManualRGBThreshold2DAlgorithm.getMinBlueThresholdAnnotation()
OptionalAnnotationNameParameter	ManualLABThreshold2DAlgorithm.getMinBlueYellowThresholdAnnotation()
OptionalAnnotationNameParameter	ManualHSBThreshold2DAlgorithm.getMinBrightnessThresholdAnnotation()
OptionalAnnotationNameParameter	ManualLABThreshold2DAlgorithm.getMinGreenRedThresholdAnnotation()
OptionalAnnotationNameParameter	ManualRGBThreshold2DAlgorithm.getMinGreenThresholdAnnotation()
OptionalAnnotationNameParameter	ManualHSBThreshold2DAlgorithm.getMinHueThresholdAnnotation()
OptionalAnnotationNameParameter	ManualLABThreshold2DAlgorithm.getMinLightnessThresholdAnnotation()
OptionalAnnotationNameParameter	ManualRGBThreshold2DAlgorithm.getMinRedThresholdAnnotation()
OptionalAnnotationNameParameter	ManualHSBThreshold2DAlgorithm.getMinSaturationThresholdAnnotation()
IntNumberRangeParameter	ManualRGBThreshold2DAlgorithm.getRedThreshold()
IntNumberRangeParameter	ManualHSBThreshold2DAlgorithm.getSaturationThreshold()
JIPipeTextAnnotationMergeMode	ManualHSBThreshold2DAlgorithm.getThresholdAnnotationStrategy()
JIPipeTextAnnotationMergeMode	ManualRGBThreshold2DAlgorithm.getThresholdAnnotationStrategy()
JIPipeTextAnnotationMergeMode	ManualLABThreshold2DAlgorithm.getThresholdAnnotationStrategy()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.iterative

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.iterative with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	IterativeThresholdByROIStatistics2DAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.iterative with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
CustomExpressionVariablesParameter	IterativeThresholdByROIStatistics2DAlgorithm.getCustomFilterVariables()
IterativeThresholdByROIStatistics2DAlgorithm.FilteringParameters	IterativeThresholdByROIStatistics2DAlgorithm.getFilteringParameters()
ImageStatisticsSetParameter	IterativeThresholdByROIStatistics2DAlgorithm.getMeasurements()
DefaultExpressionParameter	IterativeThresholdByROIStatistics2DAlgorithm.FilteringParameters.getRoiFilterExpression()
DefaultExpressionParameter	IterativeThresholdByROIStatistics2DAlgorithm.ScoreParameters.getScoreAccumulationExpression()
OptionalDefaultExpressionParameter	IterativeThresholdByROIStatistics2DAlgorithm.ScoreParameters.getScoreExpression()
IterativeThresholdByROIStatistics2DAlgorithm.ScoreParameters	IterativeThresholdByROIStatistics2DAlgorithm.getScoreParameters()
OptionalAnnotationNameParameter	IterativeThresholdByROIStatistics2DAlgorithm.getThresholdAnnotation()
JIPipeTextAnnotationMergeMode	IterativeThresholdByROIStatistics2DAlgorithm.getThresholdAnnotationStrategy()
DefaultExpressionParameter	IterativeThresholdByROIStatistics2DAlgorithm.getThresholdCombinationExpression()
DefaultExpressionParameter	IterativeThresholdByROIStatistics2DAlgorithm.FilteringParameters.getThresholdCriteriaExpression()
IntegerRange	IterativeThresholdByROIStatistics2DAlgorithm.getThresholds()
boolean	IterativeThresholdByROIStatistics2DAlgorithm.isExcludeEdgeROIs()
boolean	IterativeThresholdByROIStatistics2DAlgorithm.isMeasureInPhysicalUnits()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.local

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.local with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BernsenLocalAutoThreshold2DAlgorithm Segmenter node that thresholds via an auto threshold Based on code from Auto_Local_Threshold
class	ContrastLocalAutoThreshold2DAlgorithm Segmenter node that thresholds via an auto threshold Based on code from Auto_Local_Threshold
class	LocalAutoThreshold2DAlgorithm Segmenter node that thresholds via an auto threshold Based on code from Auto_Local_Threshold
class	NiblackLocalAutoThreshold2DAlgorithm Segmenter node that thresholds via an auto threshold Based on code from Auto_Local_Threshold
class	PhansalkarLocalAutoThreshold2DAlgorithm Segmenter node that thresholds via an auto threshold Based on code from Auto_Local_Threshold
class	SauvolaLocalAutoThreshold2DAlgorithm Segmenter node that thresholds via an auto threshold Based on code from Auto_Local_Threshold

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.local with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	BernsenLocalAutoThreshold2DAlgorithm.getContrastThreshold()
double	NiblackLocalAutoThreshold2DAlgorithm.getK()
double	PhansalkarLocalAutoThreshold2DAlgorithm.getK()
double	SauvolaLocalAutoThreshold2DAlgorithm.getK()
LocalAutoThreshold2DAlgorithm.Method	LocalAutoThreshold2DAlgorithm.getMethod()
int	LocalAutoThreshold2DAlgorithm.getModifier()
int	NiblackLocalAutoThreshold2DAlgorithm.getModifier()
double	PhansalkarLocalAutoThreshold2DAlgorithm.getP()
double	PhansalkarLocalAutoThreshold2DAlgorithm.getQ()
double	PhansalkarLocalAutoThreshold2DAlgorithm.getR()
double	SauvolaLocalAutoThreshold2DAlgorithm.getR()
int	LocalAutoThreshold2DAlgorithm.getRadius()
int	NiblackLocalAutoThreshold2DAlgorithm.getRadius()
int	ContrastLocalAutoThreshold2DAlgorithm.getRadius()
int	BernsenLocalAutoThreshold2DAlgorithm.getRadius()
int	PhansalkarLocalAutoThreshold2DAlgorithm.getRadius()
int	SauvolaLocalAutoThreshold2DAlgorithm.getRadius()
boolean	LocalAutoThreshold2DAlgorithm.isDarkBackground()
boolean	NiblackLocalAutoThreshold2DAlgorithm.isDarkBackground()
boolean	ContrastLocalAutoThreshold2DAlgorithm.isDarkBackground()
boolean	BernsenLocalAutoThreshold2DAlgorithm.isDarkBackground()
boolean	PhansalkarLocalAutoThreshold2DAlgorithm.isDarkBackground()
boolean	SauvolaLocalAutoThreshold2DAlgorithm.isDarkBackground()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.transform

Classes in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.transform with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AddBorder2DAlgorithm
class	MergeImagesAlgorithm
class	TileImage2DAlgorithm
class	TransformCrop2DAlgorithm Wrapper around ImageProcessor
class	TransformEqualCanvasSize2DAlgorithm
class	TransformEqualizeDimensionsAlgorithm
class	TransformExpandCanvas2DAlgorithm
class	TransformFlip2DAlgorithm Wrapper around ImageProcessor
class	TransformRotate2DAlgorithm Wrapper around ImageProcessor
class	TransformRotateFree2DAlgorithm Wrapper around ImageProcessor
class	TransformScale2DAlgorithm Wrapper around ImageProcessor
class	TransformScale3DAlgorithm Wrapper around ImageProcessor
class	TransformSetHyperstackDimensionsAlgorithm
class	UnTileImage2DAlgorithm
class	Warp2DAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.ij1.transform with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Anchor	TransformRotateFree2DAlgorithm.getAnchor()
Anchor	CanvasEqualizer.getAnchor()
Anchor	TransformScale2DAlgorithm.getAnchor()
Anchor	TransformEqualCanvasSize2DAlgorithm.getAnchor()
Anchor	TransformExpandCanvas2DAlgorithm.getAnchor()
double	TransformRotateFree2DAlgorithm.getAngle()
JIPipeTextAnnotationMergeMode	TileImage2DAlgorithm.getAnnotationMergeStrategy()
Color	TransformScale2DAlgorithm.getBackground()
Color	TransformRotateFree2DAlgorithm.getBackgroundColor()
Color	CanvasEqualizer.getBackgroundColor()
Color	TransformEqualCanvasSize2DAlgorithm.getBackgroundColor()
Color	TransformExpandCanvas2DAlgorithm.getBackgroundColor()
DefaultExpressionParameter	AddBorder2DAlgorithm.getBorderColor()
BorderMode	TileImage2DAlgorithm.getBorderMode()
BorderMode	AddBorder2DAlgorithm.getBorderMode()
DefaultExpressionParameter	TransformSetHyperstackDimensionsAlgorithm.getcAxis()
TransformFlip2DAlgorithm.FlipMode	TransformFlip2DAlgorithm.getFlipMode()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getImageHeightAnnotation()
OptionalAnnotationNameParameter	UnTileImage2DAlgorithm.getImageHeightAnnotation()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getImageWidthAnnotation()
OptionalAnnotationNameParameter	UnTileImage2DAlgorithm.getImageWidthAnnotation()
InterpolationMethod	TransformScale2DAlgorithm.getInterpolationMethod()
InterpolationMethod	TransformScale3DAlgorithm.getInterpolationMethod()
DefaultExpressionParameter	AddBorder2DAlgorithm.getMarginBottom()
DefaultExpressionParameter	AddBorder2DAlgorithm.getMarginLeft()
DefaultExpressionParameter	AddBorder2DAlgorithm.getMarginRight()
DefaultExpressionParameter	AddBorder2DAlgorithm.getMarginTop()
double	Warp2DAlgorithm.getMultiplier()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getNumTilesX()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getNumTilesY()
int	TileImage2DAlgorithm.getOverlapX()
int	TileImage2DAlgorithm.getOverlapY()
Margin	TransformCrop2DAlgorithm.getRoi()
TransformRotate2DAlgorithm.RotationMode	TransformRotate2DAlgorithm.getRotationDirection()
int	TransformRotate2DAlgorithm.getRotations()
TransformScale2DAlgorithm	TransformEqualizeDimensionsAlgorithm.getScale2DAlgorithm()
ScaleMode	TransformScale2DAlgorithm.getScaleMode()
ImageROITargetArea	MergeImagesAlgorithm.getTargetArea()
DefaultExpressionParameter	TransformSetHyperstackDimensionsAlgorithm.gettAxis()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getTileInsetXAnnotation()
OptionalAnnotationNameParameter	UnTileImage2DAlgorithm.getTileInsetXAnnotation()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getTileInsetYAnnotation()
OptionalAnnotationNameParameter	UnTileImage2DAlgorithm.getTileInsetYAnnotation()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getTileRealXAnnotation()
OptionalAnnotationNameParameter	UnTileImage2DAlgorithm.getTileRealXAnnotation()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getTileRealYAnnotation()
OptionalAnnotationNameParameter	UnTileImage2DAlgorithm.getTileRealYAnnotation()
int	TileImage2DAlgorithm.getTileSizeX()
int	TileImage2DAlgorithm.getTileSizeY()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getTileXAnnotation()
OptionalAnnotationNameParameter	TileImage2DAlgorithm.getTileYAnnotation()
HyperstackDimension	Warp2DAlgorithm.getVectorDimension()
WrapMode	Warp2DAlgorithm.getWrapMode()
DefaultExpressionParameter	CanvasEqualizer.getxAxis()
OptionalDefaultExpressionParameter	TransformScale2DAlgorithm.getxAxis()
NumericFunctionExpression	TransformEqualCanvasSize2DAlgorithm.getxAxis()
OptionalDefaultExpressionParameter	TransformScale3DAlgorithm.getxAxis()
NumericFunctionExpression	TransformExpandCanvas2DAlgorithm.getxAxis()
DefaultExpressionParameter	CanvasEqualizer.getyAxis()
OptionalDefaultExpressionParameter	TransformScale2DAlgorithm.getyAxis()
NumericFunctionExpression	TransformEqualCanvasSize2DAlgorithm.getyAxis()
OptionalDefaultExpressionParameter	TransformScale3DAlgorithm.getyAxis()
NumericFunctionExpression	TransformExpandCanvas2DAlgorithm.getyAxis()
DefaultExpressionParameter	TransformSetHyperstackDimensionsAlgorithm.getzAxis()
OptionalDefaultExpressionParameter	TransformScale3DAlgorithm.getzAxis()
boolean	Warp2DAlgorithm.isAbsoluteCoordinates()
boolean	TransformScale2DAlgorithm.isAvoidUnnecessaryScaling()
boolean	TransformEqualizeDimensionsAlgorithm.isCopySlices()
boolean	TransformSetHyperstackDimensionsAlgorithm.isCopySlices()
boolean	TransformEqualizeDimensionsAlgorithm.isEqualHyperstackDimensions()
boolean	TransformEqualizeDimensionsAlgorithm.isEqualWidthAndHeight()
boolean	TransformRotateFree2DAlgorithm.isExpandCanvas()
boolean	Warp2DAlgorithm.isInvertTransform()
boolean	TransformRotateFree2DAlgorithm.isOutputRoi()
boolean	Warp2DAlgorithm.isPolarCoordinates()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejalgorithms.utils

Methods in org.hkijena.jipipe.extensions.imagejalgorithms.utils with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ImageROITargetArea	SimpleImageAndRoiIteratingAlgorithm.getTargetArea()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes

Methods in org.hkijena.jipipe.extensions.imagejdatatypes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OMETIFFCompression	ImageJDataTypesSettings.getBioFormatsCompression()
boolean	ImageJDataTypesSettings.isSaveRGBWithImageJ()
boolean	ImageJDataTypesSettings.isUseBioFormats()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BioFormatsExporter
class	DisplayRangeCalibrationAlgorithm
class	ImagePropertiesToAnnotationAlgorithm Adds data annotations that contain the image properties
class	ImageTypeConverter Converts ImageJ data type into each other
class	SetBioFormatsExporterSettings

Methods in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getBitDepthAnnotation()
ImageJCalibrationMode	DisplayRangeCalibrationAlgorithm.getCalibrationMode()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getChannelSizeAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getColorSpaceAnnotation()
double	DisplayRangeCalibrationAlgorithm.getCustomMax()
double	DisplayRangeCalibrationAlgorithm.getCustomMin()
JIPipeDataByMetadataExporter	BioFormatsExporter.getExporter()
OMEExporterSettings	SetBioFormatsExporterSettings.getExporterSettings()
OMEExporterSettings	BioFormatsExporter.getExporterSettings()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getFramesSizeAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getHeightAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getImageTypeAnnotation()
Path	BioFormatsExporter.getOutputDirectory()
JIPipeDataInfoRef	ImageTypeConverter.getOutputType()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getPhysicalDimensionTAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getPhysicalDimensionValueAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getPhysicalDimensionXAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getPhysicalDimensionYAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getPhysicalDimensionZAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getPlaneNumberAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getStackSizeAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getTitleAnnotation()
OptionalAnnotationNameParameter	ImagePropertiesToAnnotationAlgorithm.getWidthAnnotation()
boolean	DisplayRangeCalibrationAlgorithm.isApplyToAllPlanes()
boolean	DisplayRangeCalibrationAlgorithm.isDuplicateImage()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms.color

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ToHSBColorSpaceConverterAlgorithm
class	ToLABColorSpaceConverterAlgorithm
class	ToRGBColorSpaceConverterAlgorithm

Methods in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms.color with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
boolean	ColorSpaceConverterAlgorithm.isReinterpret()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms.datasources

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BioFormatsImporter BioFormats importer wrapper
class	ImagePlusFromFile Loads an image data from a file via IJ.openFile()
class	ImportLUTAsRGBFromFile
class	ResultsTableFromFile Imports ResultsTableData from a file
class	ROIDataFromFile Loads ROI data from a file via IJ.openFile()
class	ROIDataFromOMEImage Loads ROI data from a file via IJ.openFile()

Methods in org.hkijena.jipipe.extensions.imagejdatatypes.algorithms.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OMEColorMode	BioFormatsImporter.getColorMode()
RectangleList	BioFormatsImporter.getCropRegions()
ResultsTableFromFile.FileFormat	ResultsTableFromFile.getFileFormat()
JIPipeDataInfoRef	ImagePlusFromFile.getGeneratedImageType()
OptionalAnnotationNameParameter	BioFormatsImporter.getSeriesAnnotation()
IntegerList	BioFormatsImporter.getSeriesToImport()
OptionalAnnotationNameParameter	ResultsTableFromFile.getSheetNameAnnotation()
StringList	ResultsTableFromFile.getSheets()
ome.xml.model.enums.DimensionOrder	BioFormatsImporter.getStackOrder()
OptionalAnnotationNameParameter	BioFormatsImporter.getTitleAnnotation()
OptionalAnnotationNameParameter	ImagePlusFromFile.getTitleAnnotation()
boolean	BioFormatsImporter.isAutoScale()
boolean	BioFormatsImporter.isConcatenate()
boolean	BioFormatsImporter.isCrop()
boolean	ImagePlusFromFile.isDeferLoading()
boolean	BioFormatsImporter.isExtractRois()
boolean	ResultsTableFromFile.isIgnoreMissingSheets()
boolean	BioFormatsImporter.isOpenAllSeries()
boolean	ImagePlusFromFile.isRemoveLut()
boolean	ImagePlusFromFile.isRemoveOverlay()
boolean	BioFormatsImporter.isSplitChannels()
boolean	BioFormatsImporter.isSplitFocalPlanes()
boolean	BioFormatsImporter.isSplitTimePoints()
boolean	BioFormatsImporter.isStitchTiles()
boolean	BioFormatsImporter.isSwapDimensions()
void	BioFormatsImporter.setToExample(JIPipeWorkbench parent)

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.compat

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.compat with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlusDataFromImageWindowImageJImporter
class	ImagePlusDataToImageWindowImageJExporter
class	OMEImageFromImageWindowImageJImporter
class	OMEImageToImageWindowImageJExporter
class	RoiManagerImageJExporter
class	RoiManagerImageJImporter

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlusData ImageJ image
class	LUTData
class	OMEImageData Data that is a representation of all information saved in Bio-Formats
class	ROIListData Contains Roi

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.color

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlusColorData A colored image without dimension.
class	ImagePlusColorHSBData HSV colored image without dimension.
class	ImagePlusColorLABData LAB colored image without dimension.
class	ImagePlusColorRGBData RGB colored image without dimension.

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2 with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus2DData 2D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2.color

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus2DColorData A colored image without dimension.
class	ImagePlus2DColorHSBData RGB colored 2D image
class	ImagePlus2DColorLABData RGB colored 2D image
class	ImagePlus2DColorRGBData RGB colored 2D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2.greyscale

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d2.greyscale with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus2DGreyscale16UData 16-bit greyscale 2D image
class	ImagePlus2DGreyscale32FData 32 bit float greyscale 2D image
class	ImagePlus2DGreyscale8UData 8-bit greyscale 2D image
class	ImagePlus2DGreyscaleData Greyscale 2D image
class	ImagePlus2DGreyscaleMaskData 8-bit mask 2D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3 with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus3DData 3D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3.color

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus3DColorData A colored image without dimension.
class	ImagePlus3DColorHSBData RGB color 3D image
class	ImagePlus3DColorLABData RGB color 3D image
class	ImagePlus3DColorRGBData RGB color 3D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3.greyscale

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d3.greyscale with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus3DGreyscale16UData 16-bit greyscale 3D image
class	ImagePlus3DGreyscale32FData 32-bit floating point greyscale 3D image
class	ImagePlus3DGreyscale8UData 8-bit greyscale 3D image
class	ImagePlus3DGreyscaleData Greyscale 3D image
class	ImagePlus3DGreyscaleMaskData 8-bit mask 3D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4 with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus4DData 4D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4.color

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus4DColorData A colored image without dimension.
class	ImagePlus4DColorHSBData RGB color 4D image
class	ImagePlus4DColorLABData RGB color 4D image
class	ImagePlus4DColorRGBData RGB color 4D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4.greyscale

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d4.greyscale with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus4DGreyscale16UData 16-bit greyscale 4D image
class	ImagePlus4DGreyscale32FData 32-bit floating point greyscale 4D image
class	ImagePlus4DGreyscale8UData 8-bit greyscale 4D image
class	ImagePlus4DGreyscaleData Greyscale 4D image
class	ImagePlus4DGreyscaleMaskData Mask 4D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5 with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus5DData 5D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5.color

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5.color with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus5DColorData A colored image without dimension.
class	ImagePlus5DColorHSBData RGB color 5D image
class	ImagePlus5DColorLABData RGB color 5D image
class	ImagePlus5DColorRGBData RGB color 5D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5.greyscale

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.d5.greyscale with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlus5DGreyscale16UData 16-bit greyscale 5D image
class	ImagePlus5DGreyscale32FData 32-bit floating point greyscale image
class	ImagePlus5DGreyscale8UData 8-bit greyscale 5D image
class	ImagePlus5DGreyscaleData Greyscale 5D image
class	ImagePlus5DGreyscaleMaskData Mask 5D image

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.fft

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.fft with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlusFFT2DData 2D image in frequency space
class	ImagePlusFFT3DData 3D image in frequency space
class	ImagePlusFFT4DData 4D image in frequency space
class	ImagePlusFFT5DData 5D image in frequency space
class	ImagePlusFFTData Image in frequency space

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.greyscale

Classes in org.hkijena.jipipe.extensions.imagejdatatypes.datatypes.greyscale with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImagePlusGreyscale16UData 16-bit greyscale image without dimension.
class	ImagePlusGreyscale32FData 32 bit float greyscale image without dimension.
class	ImagePlusGreyscale8UData 8-bit greyscale image without dimension.
class	ImagePlusGreyscaleData Greyscale image without dimension.
class	ImagePlusGreyscaleMaskData 8-bit mask without dimension.

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.parameters

Methods in org.hkijena.jipipe.extensions.imagejdatatypes.parameters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OMETIFFCompression	OMEExporterSettings.getCompression()
ome.xml.model.enums.DimensionOrder	OMEExporterSettings.getDimensionOrder()
boolean	OMEExporterSettings.isNoLUT()
boolean	OMEExporterSettings.isPadded()
boolean	OMEExporterSettings.isSaveROI()
boolean	OMEExporterSettings.isSplitC()
boolean	OMEExporterSettings.isSplitT()
boolean	OMEExporterSettings.isSplitZ()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.settings

Methods in org.hkijena.jipipe.extensions.imagejdatatypes.settings with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
RoiDrawer	ImageViewerUIRoiDisplaySettings.getRoiDrawer()
boolean	ImageViewerUIRoiDisplaySettings.isRenderROIAsOverlay()
boolean	ImageViewerUIRoiDisplaySettings.isShowROI()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imagejdatatypes.util

Methods in org.hkijena.jipipe.extensions.imagejdatatypes.util with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
boolean	ROIEditor.getCenterScale()
ROIElementDrawingMode	RoiDrawer.getDrawFilledOutlineMode()
RoiLabel	RoiDrawer.getDrawnLabel()
ROIElementDrawingMode	RoiDrawer.getDrawOutlineMode()
Color	ROIEditor.getFillColor()
OptionalColorParameter	RoiDrawer.getLabelBackground()
FontFamilyParameter	RoiDrawer.getLabelFontFamily()
Color	RoiDrawer.getLabelForeground()
int	RoiDrawer.getLabelSize()
Color	ROIEditor.getLineColor()
double	ROIEditor.getLineWidth()
double	RoiDrawer.getOpacity()
OptionalColorParameter	RoiDrawer.getOverrideFillColor()
OptionalColorParameter	RoiDrawer.getOverrideLineColor()
OptionalDoubleParameter	RoiDrawer.getOverrideLineWidth()
int	ROIEditor.getPositionC()
int	ROIEditor.getPositionT()
double	ROIEditor.getPositionX()
double	ROIEditor.getPositionY()
int	ROIEditor.getPositionZ()
String	ROIEditor.getRoiName()
double	ROIEditor.getScaleX()
double	ROIEditor.getScaleY()
boolean	RoiDrawer.isDrawOver()
boolean	RoiDrawer.isIgnoreC()
boolean	RoiDrawer.isIgnoreT()
boolean	RoiDrawer.isIgnoreZ()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imageviewer.plugins.maskdrawer

Methods in org.hkijena.jipipe.extensions.imageviewer.plugins.maskdrawer with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ImageStatisticsSetParameter	MeasurementDrawerPlugin.Settings.getStatistics()
boolean	MeasurementDrawerPlugin.Settings.isMeasureInPhysicalUnits()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.imageviewer.plugins.roimanager

Methods in org.hkijena.jipipe.extensions.imageviewer.plugins.roimanager with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ImageStatisticsSetParameter	MeasurementSettings.getStatistics()
boolean	MeasurementSettings.isMeasureInPhysicalUnits()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.multiparameters.datatypes

Classes in org.hkijena.jipipe.extensions.multiparameters.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ParametersData Stores the parameters of an algorithm

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.multiparameters.nodes

Classes in org.hkijena.jipipe.extensions.multiparameters.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AnnotationsToParametersAlgorithm
class	ConvertParametersToTableAlgorithm
class	DefineParametersAlgorithm Generates ParametersData objects
class	DefineParametersTableAlgorithm Generates ParametersData objects
class	ExtractParametersAlgorithm
class	GenerateParametersFromExpressionAlgorithm
class	MergeParametersAlgorithm
class	ParametersToAnnotationsAlgorithm

Methods in org.hkijena.jipipe.extensions.multiparameters.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeTextAnnotationMergeMode	ParametersToAnnotationsAlgorithm.getAnnotationMergeStrategy()
ParameterCollectionList	GenerateParametersFromExpressionAlgorithm.getColumns()
CustomExpressionVariablesParameter	GenerateParametersFromExpressionAlgorithm.getCustomVariables()
JIPipeDynamicParameterCollection	AnnotationsToParametersAlgorithm.getExtractedParameters()
String	GenerateParametersFromExpressionAlgorithm.Column.getKey()
OptionalAnnotationNameParameter	ExtractParametersAlgorithm.getNodeAliasIDAnnotation()
OptionalAnnotationNameParameter	ExtractParametersAlgorithm.getNodeNameAnnotation()
OptionalAnnotationNameParameter	ExtractParametersAlgorithm.getNodeUUIDAnnotation()
StringQueryExpression	ExtractParametersAlgorithm.getParameterKeyFilter()
GeneratedParameters	DefineParametersAlgorithm.getParameters()
ParameterTable	DefineParametersTableAlgorithm.getParameterTable()
JIPipeParameterTypeInfoRef	GenerateParametersFromExpressionAlgorithm.Column.getType()
DefaultExpressionParameter	GenerateParametersFromExpressionAlgorithm.Column.getValues()
boolean	AnnotationsToParametersAlgorithm.isIgnoreInvalidValues()
boolean	GenerateParametersFromExpressionAlgorithm.Column.isValuesAreJson()
void	GeneratedParameters.uiImportParameterFromGraph(JIPipeWorkbench workbench)

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.omero

Methods in org.hkijena.jipipe.extensions.omero with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
PasswordParameter	OMEROSettings.getDefaultPassword()
String	OMEROSettings.getDefaultServer()
String	OMEROSettings.getDefaultUserName()
String	OMEROSettings.getEmail()
PasswordParameter	OMEROCredentials.getPassword()
String	OMEROCredentials.getServer()
String	OMEROCredentials.getUserName()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.omero.algorithms

Classes in org.hkijena.jipipe.extensions.omero.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DownloadOMEROImageAlgorithm
class	DownloadOMEROTableAlgorithm
class	UploadOMEROImageAlgorithm
class	UploadOMEROTableAlgorithm

Methods in org.hkijena.jipipe.extensions.omero.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OMEColorMode	DownloadOMEROImageAlgorithm.getColorMode()
OMEROCredentials	UploadOMEROImageAlgorithm.getCredentials()
OMEROCredentials	DownloadOMEROTableAlgorithm.getCredentials()
OMEROCredentials	UploadOMEROTableAlgorithm.getCredentials()
OMEROCredentials	DownloadOMEROImageAlgorithm.getCredentials()
RectangleList	DownloadOMEROImageAlgorithm.getCropRegions()
JIPipeDataByMetadataExporter	UploadOMEROImageAlgorithm.getExporter()
JIPipeDataByMetadataExporter	UploadOMEROTableAlgorithm.getExporter()
OptionalStringParameter	DownloadOMEROTableAlgorithm.getFileNameAnnotation()
ome.xml.model.enums.DimensionOrder	DownloadOMEROImageAlgorithm.getStackOrder()
OptionalStringParameter	DownloadOMEROTableAlgorithm.getTagAnnotation()
OptionalStringParameter	DownloadOMEROImageAlgorithm.getTagAnnotation()
OptionalAnnotationNameParameter	DownloadOMEROImageAlgorithm.getTitleAnnotation()
AnnotationQueryExpression	UploadOMEROImageAlgorithm.getUploadedAnnotationsFilter()
boolean	DownloadOMEROTableAlgorithm.isAddKeyValuePairsAsAnnotations()
boolean	DownloadOMEROImageAlgorithm.isAddKeyValuePairsAsAnnotations()
boolean	DownloadOMEROImageAlgorithm.isAutoScale()
boolean	DownloadOMEROImageAlgorithm.isConcatenate()
boolean	DownloadOMEROImageAlgorithm.isCrop()
boolean	DownloadOMEROImageAlgorithm.isExtractRois()
boolean	DownloadOMEROImageAlgorithm.isSplitChannels()
boolean	DownloadOMEROImageAlgorithm.isSplitFocalPlanes()
boolean	DownloadOMEROImageAlgorithm.isSplitTimePoints()
boolean	DownloadOMEROImageAlgorithm.isStitchTiles()
boolean	DownloadOMEROImageAlgorithm.isSwapDimensions()
boolean	UploadOMEROImageAlgorithm.isUploadAnnotations()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.omero.datasources

Classes in org.hkijena.jipipe.extensions.omero.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	OMERODatasetReferenceDataSource
class	OMEROFindDatasetAlgorithm
class	OMEROFindGroupAlgorithm
class	OMEROFindImageAlgorithm
class	OMEROFindProjectAlgorithm
class	OMEROGroupReferenceDataSource
class	OMEROImageReferenceDataSource
class	OMEROProjectReferenceDataSource

Methods in org.hkijena.jipipe.extensions.omero.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OMEROCredentials	OMEROFindGroupAlgorithm.getCredentials()
OMEROCredentials	OMEROFindDatasetAlgorithm.getCredentials()
OMEROCredentials	OMEROFindProjectAlgorithm.getCredentials()
OMEROCredentials	OMEROFindImageAlgorithm.getCredentials()
LongList	OMERODatasetReferenceDataSource.getDatasetIds()
OptionalAnnotationNameParameter	OMEROFindDatasetAlgorithm.getDatasetNameAnnotation()
OptionalAnnotationNameParameter	OMEROFindImageAlgorithm.getDatasetNameAnnotation()
StringQueryExpression	OMEROFindDatasetAlgorithm.getDatasetNameFilters()
LongList	OMEROGroupReferenceDataSource.getGroupIds()
OptionalAnnotationNameParameter	OMEROFindGroupAlgorithm.getGroupNameAnnotation()
StringQueryExpression	OMEROFindGroupAlgorithm.getGroupNameFilters()
LongList	OMEROImageReferenceDataSource.getImageIds()
OptionalAnnotationNameParameter	OMEROFindImageAlgorithm.getImageNameAnnotation()
StringQueryExpression	OMEROFindImageAlgorithm.getImageNameFilters()
StringMapQueryExpression	OMEROFindDatasetAlgorithm.getKeyValuePairFilters()
StringMapQueryExpression	OMEROFindProjectAlgorithm.getKeyValuePairFilters()
StringMapQueryExpression	OMEROFindImageAlgorithm.getKeyValuePairFilters()
LongList	OMEROProjectReferenceDataSource.getProjectIds()
OptionalAnnotationNameParameter	OMEROFindDatasetAlgorithm.getProjectNameAnnotation()
OptionalAnnotationNameParameter	OMEROFindProjectAlgorithm.getProjectNameAnnotation()
OptionalAnnotationNameParameter	OMEROFindImageAlgorithm.getProjectNameAnnotation()
StringQueryExpression	OMEROFindProjectAlgorithm.getProjectNameFilters()
OptionalAnnotationNameParameter	OMEROFindDatasetAlgorithm.getTagAnnotation()
OptionalAnnotationNameParameter	OMEROFindProjectAlgorithm.getTagAnnotation()
OptionalAnnotationNameParameter	OMEROFindImageAlgorithm.getTagAnnotation()
StringMapQueryExpression	OMEROFindDatasetAlgorithm.getTagFilters()
StringMapQueryExpression	OMEROFindProjectAlgorithm.getTagFilters()
StringMapQueryExpression	OMEROFindImageAlgorithm.getTagFilters()
boolean	OMEROFindDatasetAlgorithm.isAddKeyValuePairsAsAnnotations()
boolean	OMEROFindProjectAlgorithm.isAddKeyValuePairsAsAnnotations()
boolean	OMEROFindImageAlgorithm.isAddKeyValuePairsAsAnnotations()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.omero.datatypes

Classes in org.hkijena.jipipe.extensions.omero.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	OMERODatasetReferenceData
class	OMEROGroupReferenceData Data that stores a reference to an OMERO project
class	OMEROImageReferenceData
class	OMEROProjectReferenceData Data that stores a reference to an OMERO project

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.omnipose

Methods in org.hkijena.jipipe.extensions.omnipose with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
StringList	OmniposeSettings.getEasyInstallerRepositories()
OptionalPythonEnvironment	OmniposeSettings.getOverridePythonEnvironment()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.omnipose.algorithms

Classes in org.hkijena.jipipe.extensions.omnipose.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	OmniposeAlgorithm
class	OmniposeTrainingAlgorithm

Methods in org.hkijena.jipipe.extensions.omnipose.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
CellposeChannelSettings	OmniposeAlgorithm.getChannelSettings()
CellposeChannelSettings	OmniposeTrainingAlgorithm.getChannelSettings()
OptionalDoubleParameter	OmniposeAlgorithm.getDiameter()
OptionalDoubleParameter	OmniposeTrainingAlgorithm.getDiameter()
OptionalAnnotationNameParameter	OmniposeAlgorithm.getDiameterAnnotation()
OmniposeSegmentationTweaksSettings	OmniposeAlgorithm.getEnhancementParameters()
CellposeGPUSettings	OmniposeAlgorithm.getGpuSettings()
CellposeGPUSettings	OmniposeTrainingAlgorithm.getGpuSettings()
DataAnnotationQueryExpression	OmniposeTrainingAlgorithm.getLabelDataAnnotation()
OmniposeModel	OmniposeAlgorithm.getModel()
int	OmniposeTrainingAlgorithm.getNumEpochs()
OptionalPythonEnvironment	OmniposeAlgorithm.getOverrideEnvironment()
OptionalPythonEnvironment	OmniposeTrainingAlgorithm.getOverrideEnvironment()
OmniposePretrainedModel	OmniposeTrainingAlgorithm.getPretrainedModel()
CellposeSegmentationOutputSettings	OmniposeAlgorithm.getSegmentationOutputSettings()
OmniposeSegmentationThresholdSettings	OmniposeAlgorithm.getThresholdParameters()
OmniposeTrainingTweaksSettings	OmniposeTrainingAlgorithm.getTweaksSettings()
boolean	OmniposeAlgorithm.isCleanUpAfterwards()
boolean	OmniposeTrainingAlgorithm.isCleanUpAfterwards()
boolean	OmniposeAlgorithm.isEnable3DSegmentation()
boolean	OmniposeTrainingAlgorithm.isEnable3DSegmentation()
boolean	OmniposeTrainingAlgorithm.isTrainSizeModel()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.omnipose.installers

Classes in org.hkijena.jipipe.extensions.omnipose.installers with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	OmniposeEasyInstaller

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.omnipose.parameters

Methods in org.hkijena.jipipe.extensions.omnipose.parameters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalDoubleParameter	OmniposeSegmentationTweaksSettings.getAnisotropy()
int	OmniposeTrainingTweaksSettings.getBatchSize()
double	OmniposeSegmentationThresholdSettings.getDiamThreshold()
double	OmniposeSegmentationThresholdSettings.getFlowThreshold()
double	OmniposeTrainingTweaksSettings.getLearningRate()
double	OmniposeSegmentationThresholdSettings.getMaskThreshold()
int	OmniposeTrainingTweaksSettings.getMinTrainMasks()
OptionalDoubleParameter	OmniposeSegmentationThresholdSettings.getStitchThreshold()
boolean	OmniposeSegmentationTweaksSettings.isCluster()
boolean	OmniposeTrainingTweaksSettings.isConcatenateDownsampledLayers()
boolean	OmniposeSegmentationTweaksSettings.isDisableResample()
boolean	OmniposeSegmentationThresholdSettings.isExcludeOnEdges()
boolean	OmniposeSegmentationTweaksSettings.isFastMode()
boolean	OmniposeTrainingTweaksSettings.isGenerateConnectedComponents()
boolean	OmniposeSegmentationTweaksSettings.isInterpolate()
boolean	OmniposeSegmentationTweaksSettings.isNetAverage()
boolean	OmniposeTrainingTweaksSettings.isUseResidualConnections()
boolean	OmniposeTrainingTweaksSettings.isUseStyleVector()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.parameters.api.enums

Methods in org.hkijena.jipipe.extensions.parameters.api.enums with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DynamicStringSetParameter	EnumParameterGenerator.getGeneratedValues()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.parameters.library.primitives

Methods in org.hkijena.jipipe.extensions.parameters.library.primitives with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
double	StringOrDouble.getDoubleValue()
double	NumberRangeParameterGenerator.getMaxNumber()
double	NumberRangeParameterGenerator.getMinNumber()
StringOrDouble.Mode	StringOrDouble.getMode()
double	NumberRangeParameterGenerator.getStepSize()
String	StringOrDouble.getStringValue()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.parameters.library.references

Methods in org.hkijena.jipipe.extensions.parameters.library.references with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalBooleanParameter	ImageJDataExportOperationRef.getActivate()
OptionalBooleanParameter	ImageJDataExportOperationRef.getAppend()
OptionalBooleanParameter	ImageJDataExportOperationRef.getDuplicate()
OptionalBooleanParameter	ImageJDataImportOperationRef.getDuplicate()
OptionalStringParameter	ImageJDataExportOperationRef.getName()
OptionalStringParameter	ImageJDataImportOperationRef.getName()
OptionalBooleanParameter	ImageJDataExportOperationRef.getNoWindows()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.parameters.library.roi

Methods in org.hkijena.jipipe.extensions.parameters.library.roi with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Anchor	FixedMargin.getAnchor()
Anchor	Margin.getAnchor()
NumericFunctionExpression	FixedMargin.getBottom()
NumericFunctionExpression	Margin.getBottom()
NumericFunctionExpression	Margin.getHeight()
NumericFunctionExpression	FixedMargin.getLeft()
NumericFunctionExpression	Margin.getLeft()
NumericFunctionExpression	FixedMargin.getRight()
NumericFunctionExpression	Margin.getRight()
NumericFunctionExpression	FixedMargin.getTop()
NumericFunctionExpression	Margin.getTop()
NumericFunctionExpression	Margin.getWidth()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.pipelinerender

Methods in org.hkijena.jipipe.extensions.pipelinerender with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	RenderPipelineRunSettings.getLabelFontSize()
OptionalIntegerParameter	RenderPipelineRunSettings.getMaxEdgeWidth()
boolean	RenderPipelineRunSettings.isRenderLabel()
boolean	RenderPipelineRunSettings.isRenderShadow()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.plots.datatypes

Classes in org.hkijena.jipipe.extensions.plots.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BarBoxAndWhiskerCategoryPlotData A box and whisker plot Series table columns: Value (Double), Category (String), Group (String) Multiple series: Yes
class	BarCategoryPlotData A bar category plot Series table columns: Value (Double), Category (String), Group (String) Multiple series: No
class	BarStatisticalCategoryPlotData A statistical bar category plot Series table columns: Value (Double), Category (String), Group (String) Multiple series: No
class	HistogramPlotData Contains data to generate a histogram plot Series table colums: Value (Numeric) Multiple series: Yes
class	LineCategoryPlotData Generates a bar category plot Series table columns: Value (Double), Category (String), Group (String) Multiple series: No
class	LineStatisticalCategoryPlotData Generates a bar category plot Series table columns: Value (Double), Category (String), Group (String) Multiple series: No
class	LineXYPlotData Generates a bar category plot Series table columns: X (Double), Y (Double) Multiple series: Yes
class	Pie2DPlotData Generates a Pie chart Series table columns: Amount (Double), Category (String) Multiple series: No
class	Pie3DPlotData Generates a Pie chart Series table columns: Amount (Double), Category (String) Multiple series: No
class	PlotData Contains all necessary data to generate a plot
class	ScatterXYPlotData A scatter XY plot Series table columns: X (Double), Y (Double) Multiple series: Yes
class	StackedBarCategoryPlotData A stacked bar plot Series table columns: Value (Double), Category (String), Group (String) Multiple series: No

Methods in org.hkijena.jipipe.extensions.plots.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
Color	PlotData.getBackgroundColor()
int	HistogramPlotData.getBinAxisFontSize()
String	HistogramPlotData.getBinAxisLabel()
int	HistogramPlotData.getBins()
int	CategoryPlotData.getCategoryAxisFontSize()
String	CategoryPlotData.getCategoryAxisLabel()
ColorMap	PlotData.getColorMap()
ColorListParameter	PlotData.getCustomColorMap()
int	PlotData.getExportHeight()
int	PlotData.getExportWidth()
Color	PlotData.getGridColor()
HistogramPlotData.HistogramType_	HistogramPlotData.getHistogramType()
int	Pie3DPlotData.getLabelFontSize()
int	Pie2DPlotData.getLabelFontSize()
int	PlotData.getLegendFontSize()
int	LineCategoryPlotData.getLineThickness()
int	LineXYPlotData.getLineThickness()
int	LineStatisticalCategoryPlotData.getLineThickness()
String	PlotDataSeries.getName()
String	PlotData.getTitle()
int	PlotData.getTitleFontSize()
int	CategoryPlotData.getValueAxisFontSize()
int	HistogramPlotData.getValueAxisFontSize()
String	CategoryPlotData.getValueAxisLabel()
String	HistogramPlotData.getValueAxisLabel()
OptionalDoubleParameter	CategoryPlotData.getValueAxisMaximum()
OptionalDoubleParameter	HistogramPlotData.getValueAxisMaximum()
OptionalDoubleParameter	CategoryPlotData.getValueAxisMinimum()
OptionalDoubleParameter	HistogramPlotData.getValueAxisMinimum()
int	XYPlotData.getxAxisFontSize()
String	XYPlotData.getxAxisLabel()
OptionalDoubleParameter	XYPlotData.getxAxisMaximum()
OptionalDoubleParameter	XYPlotData.getxAxisMinimum()
int	XYPlotData.getyAxisFontSize()
String	XYPlotData.getyAxisLabel()
OptionalDoubleParameter	XYPlotData.getyAxisMaximum()
OptionalDoubleParameter	XYPlotData.getyAxisMinimum()
boolean	PlotData.isUseCustomColorMap()
boolean	PlotData.isWithLegend()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.plots.nodes

Classes in org.hkijena.jipipe.extensions.plots.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	PlotTablesAlgorithm Deprecated. Instead, the new dynamically generated plotting should be utilized

Methods in org.hkijena.jipipe.extensions.plots.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeDynamicParameterCollection	PlotTables2Algorithm.getInputColumns()
JIPipeDynamicParameterCollection	PlotTablesAlgorithm.getInputColumns() Deprecated.
JIPipeDataInfoRef	PlotTablesAlgorithm.getPlotType() Deprecated.
PlotData	PlotTables2Algorithm.getPlotTypeParameters()
PlotData	PlotTablesAlgorithm.getPlotTypeParameters() Deprecated.
StringQueryExpression	PlotTables2Algorithm.getSeriesName()
StringQueryExpression	PlotTablesAlgorithm.getSeriesName() Deprecated.

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.processes

Methods in org.hkijena.jipipe.extensions.processes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DefaultExpressionParameter	ProcessEnvironment.getArguments()
StringQueryExpressionAndStringPairParameter.List	ProcessEnvironment.getEnvironmentVariables()
Path	ProcessEnvironment.getExecutablePathLinux()
Path	ProcessEnvironment.getExecutablePathOSX()
Path	ProcessEnvironment.getExecutablePathWindows()
ProcessEnvironment.List	ProcessesExtensionSettings.getPresets()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.python

Classes in org.hkijena.jipipe.extensions.python with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	JIPipePythonAdapterLibraryEnvironmentInstaller

Methods in org.hkijena.jipipe.extensions.python with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DefaultExpressionParameter	PythonEnvironment.getArguments()
StringList	PythonExtensionSettings.getEasyInstallerRepositories()
StringQueryExpressionAndStringPairParameter.List	PythonEnvironment.getEnvironmentVariables()
Path	PythonEnvironment.getExecutablePath()
Path	PythonPackageLibraryEnvironmentInstaller.Configuration.getInstallationPath()
Path	PythonPackageLibraryEnvironment.getLibraryDirectory()
String	PythonPackageLibraryEnvironmentInstaller.Configuration.getName()
PythonEnvironment.List	PythonExtensionSettings.getPresets()
JIPipePythonAdapterLibraryEnvironment	PythonExtensionSettings.getPythonAdapterLibraryEnvironment()
JIPipePythonAdapterLibraryEnvironment.List	PythonExtensionSettings.getPythonAdapterPresets()
PythonEnvironment	PythonExtensionSettings.getPythonEnvironment()
PythonEnvironmentType	PythonEnvironment.getType()
boolean	PythonPackageLibraryEnvironment.isProvidedByEnvironment()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.python.algorithms

Classes in org.hkijena.jipipe.extensions.python.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	IteratingJythonScriptAlgorithm An algorithm that allows to run Python code
class	IteratingPythonScriptAlgorithm An algorithm that allows to run Python code
class	JythonScriptAlgorithm An algorithm that allows to run Python code
class	MergingJythonScriptAlgorithm An algorithm that allows to run Python code
class	MergingPythonScriptAlgorithm An algorithm that allows to run Python code
class	PythonScriptAlgorithm An algorithm that allows to run Python code
class	SimpleIteratingJythonScriptAlgorithm An algorithm that allows to run Python code

Methods in org.hkijena.jipipe.extensions.python.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeTextAnnotationMergeMode	PythonScriptAlgorithm.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	IteratingPythonScriptAlgorithm.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	MergingPythonScriptAlgorithm.getAnnotationMergeStrategy()
PythonScript	JythonScriptAlgorithm.getCode()
PythonScript	SimpleIteratingJythonScriptAlgorithm.getCode()
PythonScript	PythonScriptAlgorithm.getCode()
PythonScript	MergingJythonScriptAlgorithm.getCode()
PythonScript	IteratingJythonScriptAlgorithm.getCode()
PythonScript	IteratingPythonScriptAlgorithm.getCode()
PythonScript	MergingPythonScriptAlgorithm.getCode()
OptionalPythonEnvironment	PythonScriptAlgorithm.getOverrideEnvironment()
OptionalPythonEnvironment	IteratingPythonScriptAlgorithm.getOverrideEnvironment()
OptionalPythonEnvironment	MergingPythonScriptAlgorithm.getOverrideEnvironment()
JIPipeDynamicParameterCollection	JythonScriptAlgorithm.getScriptParameters()
JIPipeDynamicParameterCollection	SimpleIteratingJythonScriptAlgorithm.getScriptParameters()
JIPipeDynamicParameterCollection	PythonScriptAlgorithm.getScriptParameters()
JIPipeDynamicParameterCollection	MergingJythonScriptAlgorithm.getScriptParameters()
JIPipeDynamicParameterCollection	IteratingJythonScriptAlgorithm.getScriptParameters()
JIPipeDynamicParameterCollection	IteratingPythonScriptAlgorithm.getScriptParameters()
JIPipeDynamicParameterCollection	MergingPythonScriptAlgorithm.getScriptParameters()
boolean	PythonScriptAlgorithm.isCleanUpAfterwards()
boolean	IteratingPythonScriptAlgorithm.isCleanUpAfterwards()
boolean	MergingPythonScriptAlgorithm.isCleanUpAfterwards()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.python.installers

Classes in org.hkijena.jipipe.extensions.python.installers with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	BasicMinicondaEnvPythonInstaller
class	BasicPortableEnvPythonInstaller
class	MinicondaEnvPythonInstaller
class	PortableEnvPythonInstaller
class	PythonEasyInstaller
class	SelectCondaEnvPythonInstaller
class	SelectSystemPythonInstaller
class	SelectVirtualEnvPythonInstaller

Methods in org.hkijena.jipipe.extensions.python.installers with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	BasicMinicondaEnvPythonInstaller.Configuration.getCondaDownloadURL()
Path	SelectCondaEnvPythonInstaller.Configuration.getCondaExecutable()
OptionalPathParameter	BasicMinicondaEnvPythonInstaller.Configuration.getCustomInstallerPath()
String	SelectCondaEnvPythonInstaller.Configuration.getEnvironmentName()
OptionalStringParameter	BasicMinicondaEnvPythonInstaller.Configuration.getForcePythonVersion()
Path	BasicMinicondaEnvPythonInstaller.Configuration.getInstallationPath()
Path	BasicPortableEnvPythonInstaller.Configuration.getInstallationPath()
String	BasicMinicondaEnvPythonInstaller.Configuration.getName()
String	SelectSystemPythonInstaller.Configuration.getName()
String	BasicPortableEnvPythonInstaller.Configuration.getName()
String	SelectCondaEnvPythonInstaller.Configuration.getName()
String	SelectVirtualEnvPythonInstaller.Configuration.getName()
OptionalPathParameter	SelectCondaEnvPythonInstaller.Configuration.getOverrideEnvironment()
OptionalPathParameter	BasicPortableEnvPythonInstaller.Configuration.getPreDownloadedArchivePath()
String	BasicPortableEnvPythonInstaller.Configuration.getPythonDownloadURL()
Path	SelectSystemPythonInstaller.Configuration.getPythonExecutable()
Path	SelectVirtualEnvPythonInstaller.Configuration.getVirtualEnvDirectory()
boolean	MinicondaEnvPythonInstaller.Configuration.isInstallNumpy()
boolean	PortableEnvPythonInstaller.Configuration.isInstallNumpy()
boolean	MinicondaEnvPythonInstaller.Configuration.isInstallPandas()
boolean	PortableEnvPythonInstaller.Configuration.isInstallPandas()
boolean	MinicondaEnvPythonInstaller.Configuration.isInstallScikitImage()
boolean	PortableEnvPythonInstaller.Configuration.isInstallScikitImage()
boolean	MinicondaEnvPythonInstaller.Configuration.isInstallScikitLearn()
boolean	PortableEnvPythonInstaller.Configuration.isInstallScikitLearn()
boolean	MinicondaEnvPythonInstaller.Configuration.isInstallTiffFile()
boolean	PortableEnvPythonInstaller.Configuration.isInstallTiffFile()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.r

Methods in org.hkijena.jipipe.extensions.r with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DefaultExpressionParameter	REnvironment.getArguments()
StringList	RExtensionSettings.getEasyInstallerRepositories()
REnvironment	RExtensionSettings.getEnvironment()
StringQueryExpressionAndStringPairParameter.List	REnvironment.getEnvironmentVariables()
REnvironment.List	RExtensionSettings.getPresets()
Path	REnvironment.getRExecutablePath()
Path	REnvironment.getRScriptExecutablePath()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.r.algorithms

Classes in org.hkijena.jipipe.extensions.r.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ImportRDatasetAlgorithm
class	IteratingRScriptAlgorithm
class	MergingRScriptAlgorithm

Methods in org.hkijena.jipipe.extensions.r.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeTextAnnotationMergeMode	MergingRScriptAlgorithm.getAnnotationMergeStrategy()
JIPipeTextAnnotationMergeMode	IteratingRScriptAlgorithm.getAnnotationMergeStrategy()
ImportRDatasetAlgorithm.Dataset	ImportRDatasetAlgorithm.getDataset()
OptionalREnvironment	ImportRDatasetAlgorithm.getOverrideEnvironment()
OptionalREnvironment	MergingRScriptAlgorithm.getOverrideEnvironment()
OptionalREnvironment	IteratingRScriptAlgorithm.getOverrideEnvironment()
RScriptParameter	MergingRScriptAlgorithm.getScript()
RScriptParameter	IteratingRScriptAlgorithm.getScript()
JIPipeDynamicParameterCollection	MergingRScriptAlgorithm.getVariables()
JIPipeDynamicParameterCollection	IteratingRScriptAlgorithm.getVariables()
boolean	MergingRScriptAlgorithm.isCleanUpAfterwards()
boolean	IteratingRScriptAlgorithm.isCleanUpAfterwards()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.r.installers

Classes in org.hkijena.jipipe.extensions.r.installers with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	REasyInstaller
class	REnvInstaller

Methods in org.hkijena.jipipe.extensions.r.installers with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalPathParameter	REnvInstaller.Configuration.getCustomInstallerPath()
Path	REnvInstaller.Configuration.getInstallationPath()
String	REnvInstaller.Configuration.getName()
String	REnvInstaller.Configuration.getRDownloadURL()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.settings

Methods in org.hkijena.jipipe.extensions.settings with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
GraphEditorUISettings.AlgorithmFinderSettings	GraphEditorUISettings.getAlgorithmFinderSettings()
DefaultExpressionParameter	DownloadSettings.DownloadEnvironment.getArguments()
GraphAutoLayout	GraphEditorUISettings.getAutoLayout()
int	AutoSaveSettings.getAutoSaveDelay()
StringList	NotificationUISettings.getBlockedNotifications()
PathList	FileChooserSettings.getBookmarks()
OptionalPathParameter	AutoSaveSettings.getCustomSavePath()
int	ImageViewerUISettings.getDefaultAnimationSpeed()
int	RuntimeSettings.getDefaultQuickRunThreads()
int	RuntimeSettings.getDefaultRunThreads()
JIPipeGraphViewMode	GraphEditorUISettings.getDefaultViewMode()
IntegerAndIntegerPairParameter.List	GeneralDataSettings.getExportedPreviewSizes()
DownloadSettings.DownloadEnvironment	DownloadSettings.getExternalDownloaderProcess()
FileChooserSettings.FileChooserType	FileChooserSettings.getFileChooserType()
Path	FileChooserSettings.getLastDataDirectory()
Path	FileChooserSettings.getLastExternalDirectory()
Path	FileChooserSettings.getLastParametersDirectory()
Path	FileChooserSettings.getLastProjectsDirectory()
int	RuntimeSettings.getLogLimit()
int	HistoryJournalSettings.getMaxEntries()
int	GeneralDataSettings.getMaxTableColumnSize()
StringList	NodeTemplateSettings.getNodeTemplateDownloadRepositories()
JIPipeNodeTemplate.List	NodeTemplateSettings.getNodeTemplates()
int	GeneralDataSettings.getPreviewSize()
ProjectsSettings.ProjectTemplateEnum	ProjectsSettings.getProjectTemplate()
StringList	ProjectsSettings.getProjectTemplateDownloadRepositories()
int	RuntimeSettings.getRealTimeRunDelay()
PathList	ProjectsSettings.getRecentJsonExtensionProjects()
PathList	ProjectsSettings.getRecentProjects()
GraphEditorUISettings.SearchSettings	GraphEditorUISettings.getSearchSettings()
OptionalIntegerParameter	NotificationUISettings.getShowAfterMinRuntime()
OptionalPathParameter	RuntimeSettings.getTempDirectory()
OptionalPathParameter	VirtualDataSettings.getTempDirectory()
JIPipeUITheme	GeneralUISettings.getTheme()
double	ImageViewerUISettings.getZoomBaseSpeed()
double	ImageViewerUISettings.getZoomDynamicSpeed()
boolean	GraphEditorUISettings.isAccurateMiniMap()
boolean	GeneralUISettings.isAddContextActionsToContextMenu()
boolean	FileChooserSettings.isAddFileExtension()
boolean	RuntimeSettings.isAllowCache()
boolean	GeneralUISettings.isAllowDefaultCollapsedParameters()
boolean	RuntimeSettings.isAllowSkipAlgorithmsWithoutInput()
boolean	ImageViewerUISettings.isAlwaysClearROIs()
boolean	GraphEditorUISettings.isAskOnDeleteCompartment()
boolean	GraphEditorUISettings.isAskOnDeleteNode()
boolean	GraphEditorUISettings.isAskOnDeleteParameter()
boolean	GraphEditorUISettings.isAutoLayoutMovesOtherNodes()
boolean	GeneralDataSettings.isAutoRemoveOutdatedCachedData()
boolean	GeneralDataSettings.isAutoSaveLastDisplay()
boolean	GeneralDataSettings.isAutoSaveLastImporter()
boolean	GraphEditorUISettings.isColorSelectedNodeEdges()
boolean	GraphEditorUISettings.isDrawArrowHeads()
boolean	GraphEditorUISettings.isDrawImprovedEdges()
boolean	GraphEditorUISettings.isDrawNodeShadows()
boolean	GraphEditorUISettings.isDrawOutsideEdges()
boolean	AutoSaveSettings.isEnableAutoSave()
boolean	NotificationUISettings.isEnableNotifications()
boolean	GraphEditorUISettings.SearchSettings.isEnableSearch()
boolean	GeneralDataSettings.isGenerateCachePreviews()
boolean	GeneralDataSettings.isGenerateResultPreviews()
boolean	VirtualDataSettings.isLargeVirtualDataTypesByDefault()
boolean	GraphEditorUISettings.isLayoutAfterAlgorithmFinder()
boolean	GraphEditorUISettings.isLayoutAfterConnect()
boolean	GeneralUISettings.isMaximizeWindows()
boolean	GeneralUISettings.isNeverAskOnClosingTabs()
boolean	GraphEditorUISettings.isNotifyInvalidDragAndDrop()
boolean	GeneralUISettings.isOpenDataWindowsAlwaysOnTop()
boolean	GeneralUISettings.isOpenUtilityWindowsAlwaysOnTop()
boolean	DownloadSettings.isPreferCustomDownloader()
boolean	RuntimeSettings.isRealTimeRunEnabled()
boolean	ProjectsSettings.isRestoreTabs()
boolean	GraphEditorUISettings.AlgorithmFinderSettings.isSearchFindExistingNodes()
boolean	GraphEditorUISettings.SearchSettings.isSearchFindExistingNodes()
boolean	GraphEditorUISettings.AlgorithmFinderSettings.isSearchFindNewNodes()
boolean	GraphEditorUISettings.SearchSettings.isSearchFindNewNodes()
boolean	GeneralUISettings.isShowIntroduction()
boolean	GeneralUISettings.isShowIntroductionTour()
boolean	GeneralUISettings.isShowParameterSearchBar()
boolean	GeneralUISettings.isShowProjectInfo()
boolean	RuntimeSettings.isShowQuickRunSetupWindow()
boolean	GraphEditorUISettings.isShowRunNodeButton()
boolean	NotificationUISettings.isShowRunNotifications()
boolean	NotificationUISettings.isShowRunOnlyIfInactive()
boolean	GraphEditorUISettings.isShowSettingsNodeButton()
boolean	TableViewerUISettings.isShowSideBar()
boolean	ImageViewerUISettings.isShowSideBar()
boolean	ExtensionSettings.isSilent()
boolean	GraphEditorUISettings.isSwitchPanningDirection()
boolean	ExtensionSettings.isValidateImageJDependencies()
boolean	ExtensionSettings.isValidateNodeTypes()
boolean	GeneralUISettings.isValidateOnSave()
boolean	VirtualDataSettings.isVirtualCache()
boolean	VirtualDataSettings.isVirtualMode()
void	AutoSaveSettings.openRestoreMenu(JIPipeWorkbench workbench)
void	AutoSaveSettings.removeDuplicateBackups(JIPipeWorkbench workbench)

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.strings

Classes in org.hkijena.jipipe.extensions.strings with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	JsonData
class	StringData A data type that contains a string
class	XMLData

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.strings.datasources

Classes in org.hkijena.jipipe.extensions.strings.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	StringDefinitionDataSource

Methods in org.hkijena.jipipe.extensions.strings.datasources with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	StringDefinitionDataSource.getValue()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.compat

Classes in org.hkijena.jipipe.extensions.tables.compat with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ResultsTableDataImageJExporter
class	ResultsTableDataImageJImporter

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.datatypes

Classes in org.hkijena.jipipe.extensions.tables.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AnnotationTableData A special kind of ResultsTableData that stores annotation columns.
class	DoubleArrayTableColumn TableColumn that contains doubles.
class	FloatArrayTableColumn TableColumn that contains doubles.
class	ResultsTableData Data containing a ResultsTable
class	RowIndexTableColumn Generates numbers from 0 to row count
class	StringArrayTableColumn TableColumn that contains doubles.
interface	TableColumn An JIPipeData type that represents a column.
class	ZeroTableColumn Generates numbers from 0 to row count

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.nodes

Classes in org.hkijena.jipipe.extensions.tables.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DefineTablesAlgorithm Algorithm that annotates all data with the same annotation
class	GenerateColumnAlgorithm Algorithm that adds or replaces a column by a generated value
class	GenerateTableFromExpressionAlgorithm Algorithm that adds or replaces a column by a generated value
class	IntegrateColumnsAlgorithm Algorithm that integrates columns
class	ModifyAndMergeTablesScript Algorithm that annotates all data with the same annotation
class	ModifyTableColumnNamesAlgorithm
class	ModifyTablesScript Algorithm that annotates all data with the same annotation
class	TablesFromScript Algorithm that annotates all data with the same annotation

Methods in org.hkijena.jipipe.extensions.tables.nodes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
PythonScript	ModifyAndMergeTablesScript.getCode()
PythonScript	TablesFromScript.getCode()
PythonScript	ModifyTablesScript.getCode()
ExpressionTableColumnGeneratorProcessorParameterList	GenerateColumnAlgorithm.getColumns()
ExpressionTableColumnGeneratorProcessorParameterList	GenerateTableFromExpressionAlgorithm.getColumns()
CustomExpressionVariablesParameter	GenerateColumnAlgorithm.getCustomFilterVariables()
OptionalIntegerParameter	GenerateColumnAlgorithm.getEnsureMinNumberOfRows()
StringQueryExpression	ModifyTableColumnNamesAlgorithm.getExpression()
int	GenerateTableFromExpressionAlgorithm.getGeneratedRows()
IntegratingTableColumnProcessorParameterList	IntegrateColumnsAlgorithm.getProcessorParameters()
JIPipeDynamicParameterCollection	ModifyAndMergeTablesScript.getScriptParameters()
JIPipeDynamicParameterCollection	TablesFromScript.getScriptParameters()
JIPipeDynamicParameterCollection	ModifyTablesScript.getScriptParameters()
ResultsTableDataList	DefineTablesAlgorithm.getTables()
boolean	GenerateColumnAlgorithm.isReplaceIfExists()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.nodes.annotations

Classes in org.hkijena.jipipe.extensions.tables.nodes.annotations with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AddAnnotationColumnsAlgorithm Algorithm that integrates columns
class	AnnotateByTablePropertiesAlgorithm
class	AnnotateDataWithTableValues
class	ConvertAnnotationTableToAnnotatedTables Algorithm that integrates columns

Methods in org.hkijena.jipipe.extensions.tables.nodes.annotations with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeTextAnnotationMergeMode	AnnotateDataWithTableValues.getAnnotationMergeMode()
JIPipeTextAnnotationMergeMode	AnnotateByTablePropertiesAlgorithm.getAnnotationMergeStrategy()
DefaultExpressionParameter	AnnotateDataWithTableValues.AnnotationSettings.getAnnotationName()
StringQueryExpression	AddAnnotationColumnsAlgorithm.getAnnotationNameFilter()
String	AddAnnotationColumnsAlgorithm.getAnnotationPrefix()
DefaultExpressionParameter	AnnotateDataWithTableValues.AnnotationSettings.getAnnotationValue()
OptionalAnnotationNameParameter	AnnotateByTablePropertiesAlgorithm.getColumnCountAnnotation()
OptionalAnnotationNameParameter	AnnotateByTablePropertiesAlgorithm.getColumnNamesAnnotation()
ParameterCollectionList	AnnotateDataWithTableValues.getGeneratedAnnotations()
OptionalAnnotationNameParameter	AnnotateByTablePropertiesAlgorithm.getRowCountAnnotation()
boolean	ConvertAnnotationTableToAnnotatedTables.isKeepAnnotationColumns()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.nodes.columns

Classes in org.hkijena.jipipe.extensions.tables.nodes.columns with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ApplyExpressionToColumnsAlgorithm Algorithm that integrates columns
class	ColumnsToAnnotationsAlgorithm
class	ColumnToNumericAlgorithm Algorithm that removes columns
class	ColumnToStringAlgorithm Algorithm that removes columns
class	ConvertColumnsAlgorithm Algorithm that integrates columns
class	RemoveColumnAlgorithm Algorithm that removes columns
class	RenameSingleColumnsAlgorithm Algorithm that removes columns
class	RenameTableColumnsAlgorithm Algorithm that removes columns
class	RenameTableColumnsToAnnotationAlgorithm Algorithm that removes columns
class	SortTableColumnsAlgorithm Algorithm that integrates columns

Methods in org.hkijena.jipipe.extensions.tables.nodes.columns with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeTextAnnotationMergeMode	ColumnsToAnnotationsAlgorithm.getAnnotationMergeStrategy()
CustomExpressionVariablesParameter	ApplyExpressionToColumnsAlgorithm.getCustomExpressionVariables()
TableCellValueQueryExpression	ColumnsToAnnotationsAlgorithm.getFilter()
StringQueryExpression	RemoveColumnAlgorithm.getFilters()
StringQueryExpression	ColumnToStringAlgorithm.getFilters()
StringQueryExpression	ColumnToNumericAlgorithm.getFilters()
ExpressionTableColumnProcessorParameterList	ApplyExpressionToColumnsAlgorithm.getProcessorParameters()
ConvertingTableColumnProcessorParameterList	ConvertColumnsAlgorithm.getProcessorParameters()
StringQueryExpressionAndStringPairParameter.List	RenameSingleColumnsAlgorithm.getRenamingEntries()
StringQueryExpressionAndStringPairParameter.List	RenameTableColumnsAlgorithm.getRenamingEntries()
StringQueryExpressionAndStringQueryPairParameter.List	RenameTableColumnsToAnnotationAlgorithm.getRenamingEntries()
JIPipeTextAnnotationMergeMode	ColumnsToAnnotationsAlgorithm.getRowMergingStrategy()
boolean	ApplyExpressionToColumnsAlgorithm.isAppend()
boolean	ConvertColumnsAlgorithm.isAppend()
boolean	RenameTableColumnsToAnnotationAlgorithm.isIgnoreMissingAnnotations()
boolean	RenameTableColumnsToAnnotationAlgorithm.isIgnoreMissingColumns()
boolean	ColumnToNumericAlgorithm.isOnlyIfPossible()
boolean	SortTableColumnsAlgorithm.isReverseSortOrder()
boolean	SortTableColumnsAlgorithm.isUseNaturalSortOrder()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.nodes.filter

Classes in org.hkijena.jipipe.extensions.tables.nodes.filter with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	FilterTableRowsAlgorithm Algorithm that integrates columns
class	FilterTablesAlgorithm Algorithm that integrates columns
class	SliceTableRowsAlgorithm

Methods in org.hkijena.jipipe.extensions.tables.nodes.filter with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
CustomExpressionVariablesParameter	FilterTableRowsAlgorithm.getCustomExpressionVariables()
DefaultExpressionParameter	FilterTableRowsAlgorithm.getFilters()
DefaultExpressionParameter	FilterTablesAlgorithm.getFilters()
IntegerRange	SliceTableRowsAlgorithm.getLimit()
boolean	FilterTablesAlgorithm.isIncludeAnnotations()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.nodes.merge

Classes in org.hkijena.jipipe.extensions.tables.nodes.merge with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	MergeColumnsAlgorithm Algorithm that integrates columns
class	MergeTableColumnsSimpleAlgorithm Algorithm that integrates columns
class	MergeTableColumnsSupplementAlgorithm Algorithm that integrates columns
class	MergeTableRowsAlgorithm Algorithm that integrates columns

Methods in org.hkijena.jipipe.extensions.tables.nodes.merge with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
StringQueryExpression	MergeTableColumnsSimpleAlgorithm.getColumnFilter()
StringQueryExpression	MergeTableColumnsSupplementAlgorithm.getColumnFilter()
StringQueryExpression	MergeTableColumnsSupplementAlgorithm.getReferenceColumns()
TableColumnNormalization	MergeTableColumnsSimpleAlgorithm.getRowNormalization()
TableColumnNormalization	MergeTableColumnsSupplementAlgorithm.getRowNormalization()
boolean	MergeTableColumnsSupplementAlgorithm.isExtendTarget()
boolean	MergeTableColumnsSupplementAlgorithm.isSkipEmptyTarget()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.nodes.rows

Classes in org.hkijena.jipipe.extensions.tables.nodes.rows with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AddMissingRowsInSeriesAlgorithm
class	ApplyExpressionPerRowAlgorithm
class	SortTableRowsAlgorithm Algorithm that integrates columns

Methods in org.hkijena.jipipe.extensions.tables.nodes.rows with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
StringQueryExpression	AddMissingRowsInSeriesAlgorithm.getCountingColumn()
CustomExpressionVariablesParameter	ApplyExpressionPerRowAlgorithm.getCustomExpressionVariables()
ExpressionTableColumnGeneratorProcessorParameterList	AddMissingRowsInSeriesAlgorithm.getDefaultValues()
double	AddMissingRowsInSeriesAlgorithm.getExpectedStep()
ExpressionTableColumnGeneratorProcessorParameterList	ApplyExpressionPerRowAlgorithm.getExpressionList()
OptionalDefaultExpressionParameter	AddMissingRowsInSeriesAlgorithm.getMaxCounter()
OptionalDefaultExpressionParameter	AddMissingRowsInSeriesAlgorithm.getMinCounter()
StringQueryExpressionAndSortOrderPairParameter.List	SortTableRowsAlgorithm.getSortOrderList()
boolean	AddMissingRowsInSeriesAlgorithm.isIgnoreEmptyTables()
boolean	SortTableRowsAlgorithm.isReverseSortOrder()
boolean	SortTableRowsAlgorithm.isUseNaturalSortOrder()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.nodes.split

Classes in org.hkijena.jipipe.extensions.tables.nodes.split with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	SplitTableByColumnsAlgorithm Algorithm that integrates columns
class	SplitTableIntoColumnsAlgorithm Algorithm that integrates columns
class	SplitTableIntoRowsAlgorithm Algorithm that integrates columns

Methods in org.hkijena.jipipe.extensions.tables.nodes.split with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
StringQueryExpression	SplitTableIntoColumnsAlgorithm.getColumnFilter()
StringQueryExpression	SplitTableByColumnsAlgorithm.getColumns()
OptionalStringParameter	SplitTableIntoColumnsAlgorithm.getGeneratedAnnotation()
boolean	SplitTableByColumnsAlgorithm.isAddAsAnnotations()
boolean	SplitTableIntoRowsAlgorithm.isAnnotateWithValues()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.nodes.transform

Classes in org.hkijena.jipipe.extensions.tables.nodes.transform with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	HistogramAlgorithm
class	MeltTableAlgorithm Algorithm that integrates columns
class	UnMeltTableAlgorithm

Methods in org.hkijena.jipipe.extensions.tables.nodes.transform with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DefaultExpressionParameter	HistogramAlgorithm.getIntegrationFunction()
TableColumnSourceExpressionParameter	HistogramAlgorithm.getKeyColumn()
OptionalStringParameter	MeltTableAlgorithm.getOutputCategoryColumnName()
String	HistogramAlgorithm.getOutputKeyColumn()
String	HistogramAlgorithm.getOutputValueColumn()
String	UnMeltTableAlgorithm.getOutputValueColumnName()
String	MeltTableAlgorithm.getOutputValueColumnName()
TableColumnSourceExpressionParameter	HistogramAlgorithm.getValueColumn()
StringQueryExpression	UnMeltTableAlgorithm.getValueColumns()
StringQueryExpression	MeltTableAlgorithm.getValueColumns()
boolean	HistogramAlgorithm.isCumulative()
boolean	HistogramAlgorithm.isNormalize()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.tables.parameters.enums

Methods in org.hkijena.jipipe.extensions.tables.parameters.enums with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
ColumnContentType	TableColumnGeneratorParameter.getGeneratedType()
JIPipeDataInfoRef	TableColumnGeneratorParameter.getGeneratorType()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.utils.algorithms

Classes in org.hkijena.jipipe.extensions.utils.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	ConverterAlgorithm Algorithm that converts any type to any other type
class	DataBatchSlicer
class	DataSlicer
class	ImportJIPipeSlotFolderAlgorithm
class	RunExpressionAlgorithm
class	SelectDataTableRowsAlgorithm
class	SetVirtualStateAlgorithm
class	SleepAlgorithm
class	SortRowsByAnnotationsAlgorithm
class	SortRowsByExpressionAlgorithm
class	ToDataStringAlgorithm
class	UsePlaceholderForMissingDataAlgorithm

Methods in org.hkijena.jipipe.extensions.utils.algorithms with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
CustomExpressionVariablesParameter	SortRowsByExpressionAlgorithm.getCustomExpressionVariables()
JIPipeDataAnnotationMergeMode	ImportJIPipeSlotFolderAlgorithm.getDataAnnotationMergeMode()
SortOrder	SortRowsByAnnotationsAlgorithm.getDefaultSortOrder()
ParameterCollectionList	SortRowsByExpressionAlgorithm.getEntries()
DefaultExpressionParameter	RunExpressionAlgorithm.getExpression()
IntegerRange	SelectDataTableRowsAlgorithm.getLimit()
JIPipeTextAnnotationMergeMode	UsePlaceholderForMissingDataAlgorithm.getPlaceholderAnnotationMergeStrategy()
IntegerRange	DataBatchSlicer.getSliceRange()
IntegerRange	DataSlicer.getSliceRange()
SortOrder	SortRowsByExpressionAlgorithm.SortEntry.getSortOrder()
StringQueryExpressionAndSortOrderPairParameter.List	SortRowsByAnnotationsAlgorithm.getSortOrderList()
SetVirtualStateAlgorithm.VirtualState	SetVirtualStateAlgorithm.getTargetState()
JIPipeTextAnnotationMergeMode	ImportJIPipeSlotFolderAlgorithm.getTextAnnotationMergeMode()
int	SleepAlgorithm.getTimeout()
DefaultExpressionParameter	SortRowsByExpressionAlgorithm.SortEntry.getValue()
OptionalAnnotationNameParameter	RunExpressionAlgorithm.getWriteToAnnotation()
JIPipeTextAnnotationMergeMode	RunExpressionAlgorithm.getWriteToAnnotationMergeStrategy()
boolean	ToDataStringAlgorithm.isDetailedDataString()
boolean	ImportJIPipeSlotFolderAlgorithm.isIgnoreImportedDataAnnotations()
boolean	ImportJIPipeSlotFolderAlgorithm.isIgnoreImportedTextAnnotations()
boolean	ImportJIPipeSlotFolderAlgorithm.isIgnoreInputDataAnnotations()
boolean	ImportJIPipeSlotFolderAlgorithm.isIgnoreInputTextAnnotations()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.utils.algorithms.datatable

Classes in org.hkijena.jipipe.extensions.utils.algorithms.datatable with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	AnnotateWithDataTableProperties
class	ExtractTableAlgorithm
class	MergeDataToTableAlgorithm
class	PullDataTableAnnotations
class	PushDataTableAnnotations

Methods in org.hkijena.jipipe.extensions.utils.algorithms.datatable with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
DataAnnotationQueryExpression	PullDataTableAnnotations.getDataAnnotationFilter()
DataAnnotationQueryExpression	PushDataTableAnnotations.getDataAnnotationFilter()
JIPipeDataAnnotationMergeMode	PullDataTableAnnotations.getDataAnnotationMergeMode()
JIPipeDataAnnotationMergeMode	PushDataTableAnnotations.getDataAnnotationMergeMode()
JIPipeTextAnnotationMergeMode	AnnotateWithDataTableProperties.getMergeMode()
JIPipeTextAnnotationMergeMode	ExtractTableAlgorithm.getMergeStrategy()
OptionalAnnotationNameParameter	AnnotateWithDataTableProperties.getNumDataAnnotationColumns()
OptionalAnnotationNameParameter	AnnotateWithDataTableProperties.getNumRowsAnnotation()
OptionalAnnotationNameParameter	AnnotateWithDataTableProperties.getNumTextAnnotationColumns()
AnnotationQueryExpression	PullDataTableAnnotations.getTextAnnotationFilter()
AnnotationQueryExpression	PushDataTableAnnotations.getTextAnnotationFilter()
JIPipeTextAnnotationMergeMode	PullDataTableAnnotations.getTextAnnotationMergeMode()
JIPipeTextAnnotationMergeMode	PushDataTableAnnotations.getTextAnnotationMergeMode()
boolean	ExtractTableAlgorithm.isMergeAnnotations()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.utils.algorithms.distribute

Classes in org.hkijena.jipipe.extensions.utils.algorithms.distribute with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	DistributeDataRandomlyByCountAlgorithm
class	DistributeDataRandomlyByPercentageAlgorithm

Methods in org.hkijena.jipipe.extensions.utils.algorithms.distribute with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OutputSlotMapParameterCollection	DistributeDataRandomlyByCountAlgorithm.getCounts()
OutputSlotMapParameterCollection	DistributeDataRandomlyByPercentageAlgorithm.getWeights()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.utils.algorithms.meta

Classes in org.hkijena.jipipe.extensions.utils.algorithms.meta with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	GetJIPipeSlotFolderAlgorithm
class	JIPipeProjectParameterDefinition
class	PathsToJIPipeProjectParametersAlgorithm
class	RunJIPipeProjectAlgorithm Runs a JIPipe project

Methods in org.hkijena.jipipe.extensions.utils.algorithms.meta with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
String	GetJIPipeSlotFolderAlgorithm.getCompartmentId()
String	GetJIPipeSlotFolderAlgorithm.getNodeId()
InputSlotMapParameterCollection	PathsToJIPipeProjectParametersAlgorithm.getParameterKeyAssignments()
Path	RunJIPipeProjectAlgorithm.getProjectFile()
String	GetJIPipeSlotFolderAlgorithm.getSlotName()
OptionalIntegerParameter	RunJIPipeProjectAlgorithm.getThreads()
void	GetJIPipeSlotFolderAlgorithm.importParametersFromProject(JIPipeWorkbench workbench)
void	JIPipeProjectParameterDefinition.importParametersFromProject(JIPipeWorkbench workbench)
void	PathsToJIPipeProjectParametersAlgorithm.importParametersFromProject(JIPipeWorkbench workbench)
boolean	RunJIPipeProjectAlgorithm.isIgnoreValidation()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.utils.algorithms.processes

Classes in org.hkijena.jipipe.extensions.utils.algorithms.processes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	RunProcessIteratingAlgorithm
class	RunProcessMergingAlgorithm

Methods in org.hkijena.jipipe.extensions.utils.algorithms.processes with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
OptionalDefaultExpressionParameter	RunProcessMergingAlgorithm.getOverrideArguments()
OptionalDefaultExpressionParameter	RunProcessIteratingAlgorithm.getOverrideArguments()
ProcessEnvironment	RunProcessMergingAlgorithm.getProcessEnvironment()
ProcessEnvironment	RunProcessIteratingAlgorithm.getProcessEnvironment()
boolean	RunProcessMergingAlgorithm.isCleanUpAfterwards()
boolean	RunProcessIteratingAlgorithm.isCleanUpAfterwards()
boolean	RunProcessMergingAlgorithm.isOutputOutputFolder()
boolean	RunProcessIteratingAlgorithm.isOutputOutputFolder()

Uses of JIPipeDocumentation in org.hkijena.jipipe.extensions.utils.datatypes

Classes in org.hkijena.jipipe.extensions.utils.datatypes with annotations of type JIPipeDocumentation

Modifier and Type	Class and Description
class	JIPipeOutputData

Uses of JIPipeDocumentation in org.hkijena.jipipe.ui.cache.exporters

Methods in org.hkijena.jipipe.ui.cache.exporters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeDataByMetadataExporter	JIPipeDataTableToFilesByMetadataExporterRun.Settings.getExporter()
boolean	JIPipeDataTableToFilesByMetadataExporterRun.Settings.isRememberSettings()
boolean	JIPipeDataTableToFilesByMetadataExporterRun.Settings.isSplitBySlotName()

Uses of JIPipeDocumentation in org.hkijena.jipipe.ui.components

Methods in org.hkijena.jipipe.ui.components with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
HTMLText	AddParameterDialog.Settings.getDescription()
String	AddParameterDialog.Settings.getId()
String	AddParameterDialog.Settings.getName()

Uses of JIPipeDocumentation in org.hkijena.jipipe.ui.grapheditor.general.properties

Methods in org.hkijena.jipipe.ui.grapheditor.general.properties with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeAdaptiveParameterSettings	JIPipeAdvancedParameterEditorUI.Settings.getAdaptiveParameterSettings()
JIPipeParameterSlotAlgorithmSettings	JIPipeAdvancedParameterEditorUI.Settings.getParameterSlotAlgorithmSettings()

Uses of JIPipeDocumentation in org.hkijena.jipipe.ui.parameters

Methods in org.hkijena.jipipe.ui.parameters with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
HTMLText	DynamicParameterEditorDialog.ParameterEntry.getDescription()
String	DynamicParameterEditorDialog.ParameterEntry.getKey()
String	DynamicParameterEditorDialog.ParameterEntry.getName()
JIPipeParameterTypeInfoRef	DynamicParameterEditorDialog.ParameterEntry.getType()

Uses of JIPipeDocumentation in org.hkijena.jipipe.ui.plotbuilder

Methods in org.hkijena.jipipe.ui.plotbuilder with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
JIPipeDynamicParameterCollection	JIPipePlotSeriesBuilder.getColumnAssignments()
PlotData	PlotEditor.getCurrentPlot()
String	JIPipePlotSeriesBuilder.getName()
JIPipeDataInfoRef	PlotEditor.getPlotType()
boolean	JIPipePlotSeriesBuilder.isEnabled()

Uses of JIPipeDocumentation in org.hkijena.jipipe.ui.quickrun

Methods in org.hkijena.jipipe.ui.quickrun with annotations of type JIPipeDocumentation

Modifier and Type	Method and Description
int	QuickRunSettings.getNumThreads()
Path	QuickRunSettings.getOutputPath()
boolean	QuickRunSettings.isExcludeSelected()
boolean	QuickRunSettings.isLoadFromCache()
boolean	QuickRunSettings.isSaveToDisk()
boolean	QuickRunSettings.isStoreIntermediateResults()
boolean	QuickRunSettings.isStoreToCache()

Uses of JIPipeDocumentation in org.hkijena.jipipe.utils

Methods in org.hkijena.jipipe.utils that return JIPipeDocumentation

Modifier and Type	Method and Description
static JIPipeDocumentation	DocumentationUtils.createDocumentation(String name, String description)
static JIPipeDocumentation	DocumentationUtils.createDocumentation(String name, String descriptionResourceURL, Class<?> descriptionResourceClass)

Methods in org.hkijena.jipipe.utils with parameters of type JIPipeDocumentation

Modifier and Type	Method and Description
static String	DocumentationUtils.getDocumentationDescription(JIPipeDocumentation documentation) Returns the documentation description string if available.
static String	DocumentationUtils.getDocumentationDescription(JIPipeDocumentation documentation, Class<?> klass) Returns the documentation description string if available.