- BaseSetHandler - Class in nfneuro.grouping
- BaseSetHandler() - Constructor in BaseSetHandler
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- BidsChannelData - Class in nfneuro.model
Container for BIDS channel data assembled by the set handlers.
- BidsChannelData() - Constructor in BidsChannelData
-
Construct an empty BidsChannelData container.
- BidsChannelFactory - Class in nfneuro.channel
Channel factory for creating BIDS-structured Nextflow channels.
- BidsChannelFactory(nextflow.Session) - Constructor in BidsChannelFactory
-
Construct a new factory bound to the given Nextflow session.
- BidsConfigAnalyzer - Class in nfneuro.config
Analyzes a bids2nf configuration map to determine which set-handler
sub-workflows are required.
- BidsConfigAnalyzer() - Constructor in BidsConfigAnalyzer
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- BidsConfigLoader - Class in nfneuro.config
Loads and validates bids2nf.yaml configuration files.
- BidsConfigLoader() - Constructor in BidsConfigLoader
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Construct a loader backed by a SnakeYAML parser.
- BidsConfigurationException(java.lang.String, java.lang.Throwable) - Constructor in BidsErrorHandler.BidsConfigurationException
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- BidsConfigValidator - Class in nfneuro.config
Validates bids2nf.yaml configuration maps.
- BidsConfigValidator.ValidationResult - Class in nfneuro.config
Holds the outcome of a configuration validation pass.
- BidsConfigValidator.ValidationResult() - Constructor in BidsConfigValidator.ValidationResult
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- BidsConfigValidator() - Constructor in BidsConfigValidator
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- BidsCsvParser - Class in nfneuro.util
Tabular parser for the output of libBIDSsh_parse_bids_to_table.
- BidsCsvParser() - Constructor in BidsCsvParser
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- BidsDataset - Class in nfneuro.model
Represents a parsed BIDS dataset.
- BidsDataset(java.lang.String) - Constructor in BidsDataset
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Construct a BidsDataset for the given root directory.
- BidsEntity - Class in nfneuro.model
Represents a single BIDS entity (key–value pair such as sub-01 or ses-BL).
- BidsEntity(java.lang.String, java.lang.String) - Constructor in BidsEntity
-
Construct a BIDS entity.
- BidsEntityUtils - Class in nfneuro.util
Utility methods for matching and grouping nfneuro.plugin.model.BidsFile objects
by their nfneuro.plugin.model.BidsEntity values.
- BidsEntityUtils() - Constructor in BidsEntityUtils
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- BidsErrorHandler - Class in nfneuro.util
Context-aware error-handling utilities for nf-bids processing.
- BidsErrorHandler.BidsConfigurationException - Class in nfneuro.util
Custom exception for BIDS configuration errors
- BidsErrorHandler.BidsProcessingException - Class in nfneuro.util
Custom exception for BIDS-specific errors
- BidsErrorHandler.BidsValidationException - Class in nfneuro.util
Custom exception for BIDS validation errors
- BidsErrorHandler() - Constructor in BidsErrorHandler
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- BidsExtension - Class in nfneuro.plugin
DSL extension point for the nf-bids Nextflow plugin.
- BidsExtension() - Constructor in BidsExtension
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- BidsFactory - Class in nfneuro.plugin
Factory that registers
BidsObserver with the Nextflow trace system.
- BidsFactory() - Constructor in BidsFactory
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- BidsFile - Class in nfneuro.model
Represents a single file entry in a BIDS dataset.
- BidsFile(java.lang.String) - Constructor in BidsFile
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Construct a BidsFile for the given path.
- BidsHandler - Class in nfneuro.channel
Fluent builder that orchestrates the full BIDS-to-channel pipeline.
- BidsHandler() - Constructor in BidsHandler
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- BidsLogger - Class in nfneuro.util
Centralized structured logging for nf-bids operations.
- BidsLogger() - Constructor in BidsLogger
-
- BidsObserver - Class in nfneuro.plugin
Nextflow trace observer for the nf-bids plugin.
- BidsObserver() - Constructor in BidsObserver
-
- bidsParentDir - Property in BidsChannelData
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- BidsParser - Class in nfneuro.parser
Main BIDS dataset parser.
- BidsParser(nextflow.Session) - Constructor in BidsParser
-
Construct a parser bound to the given Nextflow session.
- BidsPlugin - Class in nfneuro.plugin
Entry point for the nf-bids Nextflow plugin.
- BidsPlugin(org.pf4j.PluginWrapper) - Constructor in BidsPlugin
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Construct the plugin instance.
- BidsProcessingException(java.lang.String, java.lang.Throwable) - Constructor in BidsErrorHandler.BidsProcessingException
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- BidsValidationException(java.lang.String, java.lang.Throwable) - Constructor in BidsErrorHandler.BidsValidationException
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- BidsValidator - Class in nfneuro.parser
BIDS dataset validator — stub implementation (deferred to v1.1).
- BidsValidator() - Constructor in BidsValidator
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- buildAliasToEntityMap(java.lang.String) - Method in BidsEntityUtils
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- get(int) - Method in CompositeKey
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Get a specific part of the composite key by index
- getAvailableKeys(java.util.Map, List<BidsFile>) - Method in BaseSetHandler
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Get available keys for required field validation
- getBasename(List<String>) - Method in BidsFile
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Get the base name of a file without extension
- getConfigurationSummary(java.util.Map) - Method in BidsConfigAnalyzer
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Generate configuration summary for logging
- getEntities(List<String>) - Method in BidsCsvParser
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Get all entity values from a row
- getEntity(java.lang.String) - Method in BidsChannelData
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Get entity value
- getEntity(java.lang.String) - Method in BidsFile
-
- getEntityValue(java.lang.String) - Method in BidsFile
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Get entity value by name
- getExtensionType() - Method in BidsFile
-
Get extension type for categorization
- getFilename() - Method in BidsFile
-
Get filename without path
- getFilesByEntity(java.lang.String, java.lang.String) - Method in BidsDataset
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Get files by entity value
- getFilesBySuffix(java.lang.String) - Method in BidsDataset
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Get files by suffix
- getLibBidsVersion(java.lang.String) - Method in LibBidsShWrapper
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Attempt to extract the version string from a libBIDS.sh script.
- getLoopOverEntities(java.util.Map) - Method in BidsConfigAnalyzer
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Extract loop_over entities from configuration
- getMetadata(java.lang.String) - Method in BidsFile
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Get metadata value by key
- getOrdering(nfneuro.plugin.model.BidsFile, java.util.Map) - Method in BaseSetHandler
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Get sequence by entities from set config
- getOutputSuffix(java.lang.String, java.util.Map) - Method in SuffixMapper
-
Get the actual suffix that should be used in output
- getParentDir() - Method in BidsFile
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Get parent directory
- getSequenceByEntities(java.util.Map) - Method in BaseSetHandler
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Get sequence by entities from set config
- getSequenceByEntities(java.util.Map) - Method in MixedSetHandler
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Get sequential_dimension entity from config
- getSequenceByEntities(java.util.Map) - Method in NamedSetHandler
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- getSequenceByEntities(java.util.Map) - Method in PlainSetHandler
-
- getSequenceByEntities(java.util.Map) - Method in SequentialSetHandler
-
Get sequence entities from config (single or multiple)
- getSessions() - Method in BidsDataset
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Get all unique sessions in dataset
- getSetConfig(java.util.Map) - Method in BaseSetHandler
-
Get set configuration from suffix config
- getSetConfig(java.util.Map) - Method in MixedSetHandler
-
- getSetConfig(java.util.Map) - Method in NamedSetHandler
-
- getSetConfig(java.util.Map) - Method in PlainSetHandler
-
- getSetConfig(java.util.Map) - Method in SequentialSetHandler
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- getSetIndex(nfneuro.plugin.model.BidsFile, java.util.Map, java.lang.String) - Method in BaseSetHandler
-
Get set index for a file based on set configuration
- getSetIndex(nfneuro.plugin.model.BidsFile, java.util.Map, java.lang.String) - Method in MixedSetHandler
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- getSetIndex(nfneuro.plugin.model.BidsFile, java.util.Map, java.lang.String) - Method in NamedSetHandler
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- getSetIndex(nfneuro.plugin.model.BidsFile, java.util.Map, java.lang.String) - Method in PlainSetHandler
-
- getSetIndex(nfneuro.plugin.model.BidsFile, java.util.Map, java.lang.String) - Method in SequentialSetHandler
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- getSetType(java.util.Map) - Method in BaseSetHandler
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Return the set-type key present in the suffix configuration map
(one of "plain_set", "named_set", "sequential_set",
"mixed_set"), or null if none is found.
- getSidecarPath() - Method in BidsFile
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Get sidecar path (alias for jsonSidecar for compatibility)
- getStatistics() - Method in BidsDataset
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Get dataset statistics
- getSubjects() - Method in BidsDataset
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Get all unique subjects in dataset
- getSuffixData(java.lang.String) - Method in BidsChannelData
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Get suffix data
- getSuffixes() - Method in BidsChannelData
-
Get all suffixes in this channel data
- getSuffixes() - Method in BidsDataset
-
Get all unique suffixes in dataset
- getTargetSuffix(java.lang.String, java.lang.String, Map<String, Map<String, String>>) - Method in SuffixMapper
-
Get target suffix from inverted mapping for a config key
- getType() - Method in BidsFile
-
- getUniqueValues(List<BidsFile>, java.lang.String) - Method in BidsEntityUtils
-
Get all unique values for an entity across files
- groupByEntities(List<BidsFile>, List<String>) - Method in BidsEntityUtils
-
Group files by multiple entities
- groupByEntity(List<BidsFile>, java.lang.String) - Method in BidsEntityUtils
-
Group files by entity value
- groupingEntities(java.util.Map, List<String>) - Method in BaseSetHandler
-
Determine the entities used to group files for loop-over.
- groupingKey(nfneuro.plugin.model.BidsFile, List<String>) - Method in BidsEntityUtils
-
Build group key from file entities
- groupingKeyToMap(java.util.List, List<String>) - Method in BidsEntityUtils
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Build entity map from grouping key and entity names
- groupPathsByParts(List<String>, List<String>, java.util.Map) - Method in BaseSetHandler
-
Group a list of file paths by their part entity values
- groupTupleBy(groovyx.gpars.dataflow.DataflowReadChannel, groovy.lang.Closure, java.util.Map) - Method in BidsExtension
-
Group channel items by dynamically extracted keys.
- GroupTupleByOp - Class in nfneuro.channel.operations
Groups channel items by closure-extracted keys.
- GroupTupleByOp(groovyx.gpars.dataflow.DataflowReadChannel, groovy.lang.Closure) - Constructor in GroupTupleByOp
-
- groupValueByParts(java.util.List, List<String>, java.util.Map) - Method in BaseSetHandler
-