Property Detail

• static final java.lang.String ENTITY_ALIASES_RESOURCE

• static final java.lang.String NA_VALUE

Constructor Detail

• BidsEntityUtils()

Method Detail

• static java.util.Map<java.lang.String, java.lang.String> buildAliasToEntityMap(java.lang.String aliasesJsonPath)

• static java.lang.String comparisonKey(nfneuro.plugin.model.BidsFile file, java.util.List<java.lang.String> entityNames)

  Create entity comparison key Builds a key for entity-based comparison/deduplication

  Parameters:

  file - BIDS file

  entityNames - Entities to include in key

  Returns:

  Comparison key string

• static final boolean entitiesMatch(java.util.List<nfneuro.plugin.model.BidsEntity> entities, java.util.List<nfneuro.plugin.model.BidsEntity> requiredEntities, java.util.Comparator comparator)

  Check if entities match the required pattern

  reference:

  Entity matching logic from: https://github.com/agahkarakuzu/bids2nf/blob/main/modules/grouping/entity_grouping_utils.nf#L15-L30

  Parameters:

  entities - Actual entities

  requiredEntities - Required entities

  Returns:

  true if match

• static java.util.List<java.lang.String> extractEntityValues(nfneuro.plugin.model.BidsFile file, java.util.List<java.lang.String> entityNames)

  Extract entity values as ordered list

  reference:

  Entity value extraction: https://github.com/agahkarakuzu/bids2nf/blob/main/modules/grouping/entity_grouping_utils.nf#L155-L175

  Parameters:

  file - BIDS file

  entityNames - List of entity names in desired order

  Returns:

  List of entity values in same order

• static java.util.List<nfneuro.plugin.model.BidsFile> filterByEntities(java.util.List<nfneuro.plugin.model.BidsFile> files, java.util.List<nfneuro.plugin.model.BidsEntity> entityFilter)

  Filter files by entity values Returns files that match all specified entity criteria

  reference:

  Entity filtering: https://github.com/agahkarakuzu/bids2nf/blob/main/modules/grouping/entity_grouping_utils.nf#L35-L70

  Parameters:

  files - List of BIDS files

  entityFilter - Map of entity name to required value (null/"NA" = wildcard)

  Returns:

  Filtered list of files

• static java.util.List<java.lang.String> getUniqueValues(java.util.List<nfneuro.plugin.model.BidsFile> files, java.lang.String entityName)

  Get all unique values for an entity across files

  Parameters:

  files - List of BIDS files

  entityName - Entity name

  Returns:

  Sorted list of unique values (excludes "NA")

• static java.util.Map<java.lang.String, java.util.List<nfneuro.plugin.model.BidsFile>> groupByEntities(java.util.List<nfneuro.plugin.model.BidsFile> files, java.util.List<java.lang.String> entityNames)

  Group files by multiple entities Creates hierarchical grouping by multiple entity names

  Parameters:

  files - List of BIDS files

  entityNames - List of entity names to group by (in order)

  Returns:

  Nested map structure with files at leaf level

• static java.util.Map<java.lang.String, java.util.List<nfneuro.plugin.model.BidsFile>> groupByEntity(java.util.List<nfneuro.plugin.model.BidsFile> files, java.lang.String entityName)

  Group files by entity value

  reference:

  Grouping by entity: https://github.com/agahkarakuzu/bids2nf/blob/main/modules/grouping/entity_grouping_utils.nf#L75-L110

  Parameters:

  files - List of BIDS files

  entityName - Entity to group by (e.g., "acq", "dir")

  Returns:

  Map of entity value to list of files

• static java.lang.String groupingKey(nfneuro.plugin.model.BidsFile file, java.util.List<java.lang.String> entities)

  Build group key from file entities Normalizes entity names from long to short format before lookup. Config uses long names (subject, session) but files store short names (sub, ses).

  Parameters:

  file - BIDS file

  entities - Entities to include in key (may be long or short names)

  Returns:

  Group key string

• static java.util.Map<java.lang.String, nfneuro.plugin.model.BidsEntity> groupingKeyToMap(java.util.List groupingKeyList, java.util.List<java.lang.String> entityNames)

  Build entity map from grouping key and entity names

  Parameters:

  groupingKeyList - Tuple key from channel

  entityNames - List of entity names

  Returns:

  Map of entity name to value

• static boolean hasConsistentEntities(java.util.List<nfneuro.plugin.model.BidsFile> files, java.util.List<java.lang.String> entityNames)

  Check if files have consistent entity values Validates that all files in a group have the same value for given entities

  Parameters:

  files - List of BIDS files

  entityNames - Entity names to check

  Returns:

  true if all files have same values for these entities

• static boolean hasRequiredEntities(nfneuro.plugin.model.BidsFile file, java.util.List<java.lang.String> requiredEntities)

  Validate required entities are present

  Parameters:

  file - BIDS file

  requiredEntities - List of entity names that must be present

  Returns:

  true if all required entities exist

• static java.lang.String normalizeEntityKey(java.lang.String key, java.util.Map<java.lang.String, java.lang.String> aliasToEntity)

• static java.util.Map<java.lang.String, java.lang.String> normalizeEntityMap(java.util.Map values, java.util.Map<java.lang.String, java.lang.String> aliasToEntity)

• static java.lang.String normalizeEntityValue(java.lang.String entityKey, java.lang.String value, java.util.Map<java.lang.String, java.lang.String> aliasToEntity)

• static java.util.List<nfneuro.plugin.model.BidsFile> sortByEntity(java.util.List<nfneuro.plugin.model.BidsFile> files, java.lang.String entityName)

  Sort files by entity value Sorts files based on entity values (numeric if possible, lexicographic otherwise)

  Parameters:

  files - List of BIDS files

  entityName - Entity to sort by

  Returns:

  Sorted list of files

• static java.lang.String toEntityString(nfneuro.plugin.model.BidsFile file, java.util.List<java.lang.String> entityNames)

  Create entity string representation Builds a readable string like "sub-01_ses-01_run-1"

  Parameters:

  file - BIDS file

  entityNames - Entities to include

  Returns:

  Entity string