Constructor Detail

• BaseSetHandler()

Method Detail

• protected java.util.List applyFlatOrdering(java.util.Map files)

• protected java.util.List applyFlatOrdering(java.util.List files)

• protected java.util.List applyHierarchicalOrdering(java.util.Map files)

• protected java.util.List applyHierarchicalOrdering(java.util.List files)

• protected java.util.Map applyPartsGrouping(java.util.Map nestedMap, java.util.List<java.lang.String> partsConfig, java.util.List<nfneuro.plugin.model.BidsFile> allFiles, java.lang.String datasetRoot)

  Apply parts grouping to a nested data map Transforms file lists/values grouped by extension to also group by BIDS 'part' entity. Parts represent subcomponents of complex MRI data (e.g., mag/phase, real/imag). Input structure examples: {nii: ["path1", "path2"]} or {nii: "path"} Output structure with parts: {nii: [{mag: "path1_mag", phase: "path1_phase"}, {mag: "path2_mag", phase: "path2_phase"}]}

  Parameters:

  nestedMap - Map of extension type to file path(s) - {nii: [...], json: [...]}

  partsConfig - List of part values to group by (e.g., ["mag", "phase"])

  allFiles - All BidsFile objects for extracting part entity values

  datasetRoot - Root path for computing relative paths

  Returns:

  Transformed map with parts grouping applied where applicable

• protected int compareSequenceValues(java.lang.String a, java.lang.String b)

  Compare sequence values for sorting Attempts numeric comparison first by extracting numbers from entity values. For example, "echo-10" and "echo-2" will be compared as 10 and 2 (not alphabetically). Falls back to string comparison if values are not numeric.

  Parameters:

  a - First value to compare

  b - Second value to compare

  Returns:

  Negative if a < b, positive if a > b, zero if equal

• protected int compareSequenceValues(java.util.List a, java.util.List b)

• protected java.util.Set<java.lang.String> consumedEntities(java.util.Map config)

  Collect the entities consumed internally by this set type across all configurations, normalized to their short form.

  A consumed entity is one whose value varies across the files that are merged into a single emitted item (for example a sequential set's by_entity/by_entities, or a mixed set's sequential_dimension). Such entities must be kept out of both the grouping key and the emitted meta so files spanning that dimension collapse into a single item and fuse with the other results instead of being split into one item per value.

  Set types without a sequenced dimension (plain and named sets) return an empty set, making this a no-op for them.

  Parameters:

  config - Full configuration map

  Returns:

  Set of normalized entity names consumed by this set type

• protected java.util.List<nfneuro.plugin.model.BidsFile> filterBySuffix(java.util.List<nfneuro.plugin.model.BidsFile> files, java.lang.String suffix)

  Filter files by suffix

  Parameters:

  files - All BIDS files

  suffix - Target suffix

  Returns:

  Filtered files

• protected java.util.Map findMatchingGrouping(nfneuro.plugin.model.BidsFile file, java.util.Map config, java.util.Map<java.lang.String, java.util.Map<java.lang.String, java.lang.String>> suffixMapping)

  Find matching grouping pattern for given file Tries all candidate config keys for the file's suffix and returns the first one that passes all validation checks.

  reference:

  findMatchingGrouping function: https://github.com/agahkarakuzu/bids2nf/blob/main/modules/grouping/entity_grouping_utils.nf#L1-L35

  Parameters:

  file - BIDS file

  config - Configuration

  suffixMapping - Suffix to config key mapping (inverted: configKey -> targetSuffix)

  Returns:

  Map with configKey and setConfig if match found, null otherwise

• protected java.util.Set<java.lang.String> getAvailableKeys(java.util.Map subset, java.util.List<nfneuro.plugin.model.BidsFile> allFiles)

  Get available keys for required field validation For named sets: returns keys from subset.files (named groups like 'ap', 'pa') For sequential/plain sets: returns file types/extensions (like 'nii', 'json', 'bval') For mixed sets: returns both named groups and file types

  Parameters:

  subset - The set data structure

  allFiles - All files for this suffix

  Returns:

  Set of available keys

• protected java.util.Map<java.lang.String, java.util.List<java.lang.String>> getOrdering(nfneuro.plugin.model.BidsFile file, java.util.Map setConfig)

  Get sequence by entities from set config

  Parameters:

  file - BIDS file

  setConfig - Set configuration

  Returns:

  List of entities to sequence by

• protected abstract java.util.List<java.lang.String> getSequenceByEntities(java.util.Map setConfig)

  Get sequence by entities from set config

  Parameters:

  setConfig - Set configuration

  Returns:

  List of entities to sequence by

• protected abstract java.util.Map getSetConfig(java.util.Map suffixConfig)

  Get set configuration from suffix config

  Parameters:

  suffixConfig - Configuration for specific suffix

  Returns:

  Set configuration (plain_set, named_set, etc.)

• protected abstract java.util.Map getSetIndex(nfneuro.plugin.model.BidsFile file, java.util.Map setConfig, java.lang.String configKey)

  Get set index for a file based on set configuration

  Parameters:

  file - BIDS file

  setConfig - Set configuration

  configKey - Configuration key (for suffix_maps_to support)

  Returns:

  Set index containing both fileSuffix and configKey

• static final java.lang.String getSetType(java.util.Map suffixConfig)

  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.

  Parameters:

  suffixConfig - the per-suffix configuration map entry

  Returns:

  the matched set-type string, or null

• protected java.util.List groupPathsByParts(java.util.List<java.lang.String> paths, java.util.List<java.lang.String> partsConfig, java.util.Map basenameToFile)

  Group a list of file paths by their part entity values Uses the basenameToFile lookup map to find properly parsed BidsFile objects. Groups files by their basename (excluding part entity) and creates part-grouped maps.

  Parameters:

  paths - List of relative file paths to group

  partsConfig - List of part values (e.g., ["mag", "phase"])

  basenameToFile - Map of basename to BidsFile objects

• protected java.util.List groupValueByParts(java.lang.String value, java.util.List<java.lang.String> partsConfig, java.util.Map basenameToFile)

• protected java.util.List groupValueByParts(java.util.List value, java.util.List<java.lang.String> partsConfig, java.util.Map basenameToFile)

• protected java.util.List<java.lang.String> groupingEntities(java.util.Map config, java.util.List<java.lang.String> loopOverEntities)

  Determine the entities used to group files for loop-over.

  By default this is the full list of loop-over entities. Handlers whose sets consume an entity internally (for example a mixed_set's sequential_dimension) override this to remove those entities so that files spanning the consumed dimension are collapsed into a single group and fused with the other results.

  Parameters:

  config - Full configuration map

  loopOverEntities - Configured loop-over entities

  Returns:

  Entities to group files by

• protected java.lang.String logGroup()

• protected void logProcessingStats(int processedCount, int filteredCount)

  Log processing statistics

  Parameters:

  handlerName - Name of handler

  processedCount - Files processed

  filteredCount - Files filtered

• protected abstract void packFileIntoSet(java.util.Map sets, java.util.Map allFiles, java.util.Map index, nfneuro.plugin.model.BidsFile file, java.util.Map ordering)

  Pack file into set structure

  Parameters:

  sets - Set structure to populate

  allFiles - Map of associated files

  index - Set index for the file

  file - BIDS file to pack

  ordering - Ordering information for sequencing

• groovyx.gpars.dataflow.DataflowQueue process(java.lang.String datasetRoot, java.util.List<nfneuro.plugin.model.BidsFile> bidsFiles, java.util.Map config, java.util.List<java.lang.String> loopOverEntities, java.util.Map<java.lang.String, java.util.Map<java.lang.String, java.lang.String>> suffixMapping)

• protected abstract java.util.List<nfneuro.plugin.model.BidsChannelData> processGroup(java.lang.String datasetRoot, java.util.Map plainSets, java.util.Map allFiles, java.util.Map config, java.util.List<java.lang.String> loopOverEntities, java.util.Map suffixMapping)

• protected abstract java.lang.String setName()

  Get set name

  Returns:

  Name of the set type (e.g., "plain_set", "named_set")

• protected boolean validateRequiredFileCount(java.util.List<nfneuro.plugin.model.BidsFile> files, java.lang.Integer requiredCount)

  Validate required files are present in group

  reference:

  validateRequiredFiles function: https://github.com/agahkarakuzu/bids2nf/blob/main/modules/grouping/validation_utils.nf#L1-L25

  Parameters:

  files - File list

  requiredCount - Minimum required files

  Returns:

  true if valid